The pixels in image data now has been categorized into five regions according to the initial setting of segmentation (spectra_segments_per_file=5). The rainbow shaped bovine lens segmentation image (on the left panel) shows a unique statistical classification based on the mz features of each region (on the right panel).
The identification will take place on the mean spectra of each region. To check the peptide mass fingerprint (PMF) matching quality, you could locate the PMF spectrum matching plot of each individual region.
library(magick)
@@ -572,20 +573,20 @@ 0.4 Identification result visulas
## # A tibble: 1 x 7
## format width height colorspace matte filesize density
## <chr> <int> <int> <chr> <lgl> <int> <chr>
-## 1 PNG 1980 1080 sRGB FALSE 17113 72x72
-
+## 1 PNG 1980 1080 sRGB FALSE 17165 72x72
list of Peptides and proteins of each region has also been created so that you may check each individual region’s result.
peptide_pmf_result<-read.csv(paste0(wd,datafile," ID/Peptide_segment_PMF_RESULT_3.csv"))
head(peptide_pmf_result)## # A tibble: 6 x 16
## Protein mz Peptide adduct formula isdecoy pepmz charge mz_align Score
## <int> <dbl> <fct> <fct> <fct> <int> <dbl> <int> <dbl> <dbl>
-## 1 9 1467. GGNELD~ M+H C60H96~ 0 1466. 1 1467. 0.369
-## 2 9 1323. QEDQLQ~ M+H C55H88~ 0 1322. 1 1323. 0.573
+## 1 9 1323. QIDQKE~ M+H C55H88~ 0 1322. 1 1323. 0.573
+## 2 9 1467. GGNELD~ M+H C60H96~ 0 1466. 1 1467. 0.369
## 3 9 1469. NEEPSS~ M+H C62H94~ 0 1468. 1 1469. 3.44
-## 4 9 1323. QIDQKE~ M+H C55H88~ 0 1322. 1 1323. 0.573
-## 5 13 1493. MDPTDA~ M+H C62H98~ 0 1492. 1 1493. 2.43
-## 6 13 1359. LKELEV~ M+H C58H10~ 0 1358. 1 1359. 0.542
+## 4 9 1323. QEDQLQ~ M+H C55H88~ 0 1322. 1 1323. 0.573
+## 5 13 1359. LKELEV~ M+H C58H10~ 0 1358. 1 1359. 0.542
+## 6 13 1493. MDPTDA~ M+H C62H98~ 0 1492. 1 1493. 2.43
## # ... with 6 more variables: Rank <int>, Intensity <dbl>,
## # moleculeNames <fct>, Region <int>, Delta_ppm <dbl>, desc <fct>protein_pmf_result<-read.csv(paste0(wd,datafile," ID/Protein_segment_PMF_RESULT_3.csv"))
@@ -593,12 +594,12 @@ 0.4 Identification result visulas
## # A tibble: 6 x 9
## Protein Proscore isdecoy Intensity Score peptide_count Protein_coverage
## <int> <dbl> <int> <dbl> <dbl> <int> <dbl>
-## 1 10134 0.147 0 1189179. 1.30 5 0.0978
-## 2 10204 0.179 0 167823. 0.912 4 0.198
-## 3 10370 0.169 0 990324. 2.06 3 0.0719
-## 4 10628 0.0617 0 340804. 1.06 2 0.0553
-## 5 10691 0.125 0 442322. 1.36 3 0.0861
-## 6 10754 0.0699 0 93787. 2.31 1 0.0321
+## 1 10003 0.0552 0 88609. 0.855 2 0.0685
+## 2 1002 0.0556 0 580348. 0.843 4 0.0600
+## 3 10112 0.100 0 641587. 0.889 2 0.102
+## 4 10134 0.0914 0 1455153. 1.05 4 0.0745
+## 5 10204 0.180 0 167823. 0.912 4 0.198
+## 6 10370 0.170 0 990324. 2.06 3 0.0719
## # ... with 2 more variables: Intensity_norm <dbl>, desc <fct>
## # A tibble: 6 x 16
## Protein mz Peptide adduct formula isdecoy pepmz charge mz_align Score
## <int> <dbl> <fct> <fct> <fct> <int> <dbl> <int> <dbl> <dbl>
-## 1 393 1881. GMSIDQ~ M+H C81H13~ 0 1880. 1 1881. 2.56
-## 2 393 1301. RPAEIY~ M+H C55H90~ 0 1300. 1 1301. 0.765
-## 3 393 1170. LGALWV~ M+H C54H89~ 0 1169. 1 1170. 0.224
-## 4 452 1837. DGQVIN~ M+H C74H11~ 0 1836. 1 1837. 1.72
-## 5 452 932. LLEGEE~ M+H C38H66~ 0 931. 1 932. 1.78
-## 6 452 2203. EMEENF~ M+H C92H14~ 0 2202. 1 2203. 0.631
+## 1 148 1138. MVEFAG~ M+H C50H81~ 0 1137. 1 1138. 1.39
+## 2 148 2594. AFIVWN~ M+H C121H1~ 0 2593. 1 2594. 2.31
+## 3 216 1881. ITTLQQ~ M+H C77H13~ 0 1880. 1 1881. 1.64
+## 4 216 1458. ELELGE~ M+H C61H10~ 0 1457. 1 1458. 0.794
+## 5 393 1170. LGALWV~ M+H C54H89~ 0 1169. 1 1170. 0.224
+## 6 393 1301. RPAEIY~ M+H C55H90~ 0 1300. 1 1301. 0.765
## # ... with 6 more variables: Rank <int>, Intensity <dbl>,
## # moleculeNames <fct>, Region <int>, Delta_ppm <dbl>, desc <fct>The details of protein/peptide identification process has been save to the folder named by the segmentation:
@@ -651,7 +652,7 @@
p_FDR_peptide<-image_read(paste0(wd,datafile," ID/3/FDR.png"))
p_FDR_protein<-image_read(paste0(wd,datafile," ID/3/protein_FDR.png"))
p_FDR_peptide_his<-image_read(paste0(wd,datafile," ID/3/Peptide_Score_histogram_target-decoy.png"))
@@ -662,7 +663,7 @@ 0.5 Scoring system for protein an
## format width height colorspace matte filesize density
## <chr> <int> <int> <chr> <lgl> <int> <chr>
## 1 PNG 1920 480 sRGB FALSE 0 72x72
you will also find a Matching_Score_vs_mz plots for further investigation on peptide matching quality.
library(magick)
#plot Matching_Score_vs_mz
@@ -672,7 +673,7 @@ 0.5 Scoring system for protein an
## format width height colorspace matte filesize density
## <chr> <int> <int> <chr> <lgl> <int> <chr>
## 1 PNG 480 480 sRGB FALSE 54177 72x72
p_cluster3<-image_read(paste0(wd,"/Summary folder/cluster Ion images/5479_cluster_imaging.png"))
print(p_cluster3)## # A tibble: 1 x 7
## format width height colorspace matte filesize density
## <chr> <int> <int> <chr> <lgl> <int> <chr>
## 1 PNG 1980 385 sRGB TRUE 390494 118x118
R Packages used in this project:
+viridisLite(Garnier 2018)
rcdklibs(Guha 2017)
rJava(Urbanek 2019)
data.table(Dowle and Srinivasan 2019)
RColorBrewer(Neuwirth 2014)
magick(Ooms 2019)
ggplot2(Wickham 2016)
dplyr(Wickham et al. 2019)
stringr(Wickham 2019)
protViz(Panse and Grossmann 2019)
cleaver(Gibb 2019)
Biostrings(Pag�s et al. 2019)
IRanges(Lawrence et al. 2013)
Cardinal(Bemis et al. 2015)
tcltk(R Core Team 2019)
BiocParallel(Morgan et al. 2019)
spdep(Bivand and Wong 2018)
FTICRMS(Barkauskas 2012)
UniProt.ws(Carlson 2019)
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
@@ -741,12 +767,71 @@ 0.7 Session information
## [28] grid_3.6.1 glue_1.3.1 Biobase_2.44.0
## [31] R6_2.4.0 fansi_0.4.0 tcltk_3.6.1
## [34] XML_3.98-1.20 survival_2.44-1.1 BiocParallel_1.18.1
-## [37] pacman_0.5.1 rmarkdown_1.16 purrr_0.3.2
+## [37] pacman_0.5.1 rmarkdown_1.18 purrr_0.3.2
## [40] magrittr_1.5 backports_1.1.5 MASS_7.3-51.4
## [43] codetools_0.2-16 htmltools_0.4.0 BiocGenerics_0.30.0
## [46] splines_3.6.1 assertthat_0.2.1 utf8_1.1.4
## [49] stringi_1.4.3 doParallel_1.0.15 crayon_1.3.4End of the tutorial, Enjoy~
+Barkauskas, Don. 2012. FTICRMS: Programs for Analyzing Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Data. https://CRAN.R-project.org/package=FTICRMS.
+Bemis, Kyle D., April Harry, Livia S. Eberlin, Christina Ferreira, Stephanie M. van de Ven, Parag Mallick, Mark Stolowitz, and Olga Vitek. 2015. “Cardinal: An R Package for Statistical Analysis of Mass Spectrometry-Based Imaging Experiments.” Bioinformatics. https://doi.org/10.1093/bioinformatics/btv146.
+Bivand, Roger, and David W. S. Wong. 2018. “Comparing Implementations of Global and Local Indicators of Spatial Association.” TEST 27 (3): 716–48. https://doi.org/10.1007/s11749-018-0599-x.
+Carlson, Marc. 2019. UniProt.ws: R Interface to Uniprot Web Services.
+Dowle, Matt, and Arun Srinivasan. 2019. Data.table: Extension of ‘Data.frame‘. https://CRAN.R-project.org/package=data.table.
+Garnier, Simon. 2018. ViridisLite: Default Color Maps from ’Matplotlib’ (Lite Version). https://CRAN.R-project.org/package=viridisLite.
+Gibb, Sebastian. 2019. Cleaver: Cleavage of Polypeptide Sequences. https://github.com/sgibb/cleaver/.
+Guha, Rajarshi. 2017. Rcdklibs: The Cdk Libraries Packaged for R. https://CRAN.R-project.org/package=rcdklibs.
+Lawrence, Michael, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, and Vincent Carey. 2013. “Software for Computing and Annotating Genomic Ranges.” PLoS Computational Biology 9 (8). https://doi.org/10.1371/journal.pcbi.1003118.
+Morgan, Martin, Valerie Obenchain, Michel Lang, Ryan Thompson, and Nitesh Turaga. 2019. BiocParallel: Bioconductor Facilities for Parallel Evaluation. https://github.com/Bioconductor/BiocParallel.
+Neuwirth, Erich. 2014. RColorBrewer: ColorBrewer Palettes. https://CRAN.R-project.org/package=RColorBrewer.
+Ooms, Jeroen. 2019. Magick: Advanced Graphics and Image-Processing in R. https://CRAN.R-project.org/package=magick.
+Pag�s, H., P. Aboyoun, R. Gentleman, and S. DebRoy. 2019. Biostrings: Efficient Manipulation of Biological Strings.
+Panse, Christian, and Jonas Grossmann. 2019. ProtViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics.
+R Core Team. 2019. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
+Urbanek, Simon. 2019. RJava: Low-Level R to Java Interface. https://CRAN.R-project.org/package=rJava.
+Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.
+———. 2019. Stringr: Simple, Consistent Wrappers for Common String Operations. https://CRAN.R-project.org/package=stringr.
+Wickham, Hadley, Romain Fran�ois, Lionel Henry, and Kirill Muller. 2019. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.
+
@@ -193,12 +194,12 @@ head(peptide_pmf_result)
## # A tibble: 6 x 16
## Protein mz Peptide adduct formula isdecoy pepmz charge mz_align Score
## 
+
+## References
+R Packages used in this project:
+
+ + viridisLite[@viridisLite]
+
+ + rcdklibs[@rcdklibs]
+
+ + rJava[@rJava]
+
+ + data.table[@data.table]
+
+ + RColorBrewer[@RColorBrewer]
+
+ + magick[@magick]
+
+ + ggplot2[@ggplot2]
+
+ + dplyr[@dplyr]
+
+ + stringr[@stringr]
+
+ + protViz[@protViz]
+
+ + cleaver[@cleaver]
+
+ + Biostrings[@Biostrings]
+
+ + IRanges[@IRanges]
+
+ + Cardinal[@Cardinal]
+
+ + tcltk[@tcltk]
+
+ + BiocParallel[@BiocParallel]
+
+ + spdep[@spdep1]
+
+ + FTICRMS[@FTICRMS]
+
+ + UniProt.ws[@UniProt.ws]
+
+
+
## Session information
@@ -448,7 +493,7 @@ sessionInfo()
## [28] grid_3.6.1 glue_1.3.1 Biobase_2.44.0
## [31] R6_2.4.0 fansi_0.4.0 tcltk_3.6.1
## [34] XML_3.98-1.20 survival_2.44-1.1 BiocParallel_1.18.1
-## [37] pacman_0.5.1 rmarkdown_1.16 purrr_0.3.2
+## [37] pacman_0.5.1 rmarkdown_1.18 purrr_0.3.2
## [40] magrittr_1.5 backports_1.1.5 MASS_7.3-51.4
## [43] codetools_0.2-16 htmltools_0.4.0 BiocGenerics_0.30.0
## [46] splines_3.6.1 assertthat_0.2.1 utf8_1.1.4
@@ -457,6 +502,4 @@ sessionInfo()
-
-
End of the tutorial, Enjoy~
diff --git a/README_files/figure-html/CLuster imaging-1.png b/README_files/figure-html/CLuster imaging-1.png
index 0ebe1fb..0bf0535 100644
Binary files a/README_files/figure-html/CLuster imaging-1.png and b/README_files/figure-html/CLuster imaging-1.png differ
diff --git a/README_files/figure-html/CLuster imaging-2.png b/README_files/figure-html/CLuster imaging-2.png
index f19103a..a173894 100644
Binary files a/README_files/figure-html/CLuster imaging-2.png and b/README_files/figure-html/CLuster imaging-2.png differ
diff --git a/README_files/figure-html/FDR plot-1.png b/README_files/figure-html/FDR plot-1.png
index bec6492..73a0651 100644
Binary files a/README_files/figure-html/FDR plot-1.png and b/README_files/figure-html/FDR plot-1.png differ
diff --git a/README_files/figure-html/FDR plot-2.png b/README_files/figure-html/FDR plot-2.png
index bfa5654..94a7f6a 100644
Binary files a/README_files/figure-html/FDR plot-2.png and b/README_files/figure-html/FDR plot-2.png differ
diff --git a/README_files/figure-html/VisulazeKmean-1.png b/README_files/figure-html/VisulazeKmean-1.png
index fca1e96..80ecb16 100644
Binary files a/README_files/figure-html/VisulazeKmean-1.png and b/README_files/figure-html/VisulazeKmean-1.png differ
diff --git a/README_files/figure-html/p_Matching_Score_vs_mz plot-1.png b/README_files/figure-html/p_Matching_Score_vs_mz plot-1.png
index 8cd91a4..d4a282b 100644
Binary files a/README_files/figure-html/p_Matching_Score_vs_mz plot-1.png and b/README_files/figure-html/p_Matching_Score_vs_mz plot-1.png differ
diff --git a/README_files/figure-html/unnamed-chunk-1-1.png b/README_files/figure-html/unnamed-chunk-1-1.png
index f7ea2d1..d14bc52 100644
Binary files a/README_files/figure-html/unnamed-chunk-1-1.png and b/README_files/figure-html/unnamed-chunk-1-1.png differ
diff --git a/man/training_cmd.Rmd b/man/training_cmd.Rmd
index 3150598..ff1c3a4 100644
--- a/man/training_cmd.Rmd
+++ b/man/training_cmd.Rmd
@@ -36,11 +36,12 @@ imaging_identification(Digestion_site="([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=
imaging_identification(Digestion_site="([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))",Fastadatabase="uniprot-Human.fasta",output_candidatelist=T,spectra_segments_per_file=4,use_previous_candidates=T,ppm=10,FDR_cutoff = 0.1,PMF_analysis=T,plot_cluster_image_grid=T,Protein_desc_of_interest=c("Histone ","GN=MBP","ACTIN"))
```{r Citations}
-library(gtools)
-dependencies<-gtools::getDependencies("HiTMaP", dependencies = c("Depends", "Imports", "LinkingTo"), installed=TRUE, available=TRUE, base=FALSE, recommended=FALSE)
-citations<-(lapply(dependencies, citation))
-#writeLines(citations,"citations.BIB")
-citations
+library(pacman)
+p_load("gtools")
+dependencies<-gtools::getDependencies("HiTMaP", dependencies = c("Depends", "Imports", "LinkingTo"), installed=TRUE, available=TRUE,
+ base=TRUE, recommended=FALSE)
+p_load("bibtex")
+write.bib(dependencies, file="references")
```
#Bovin lens FTICR
diff --git a/references.bib b/references.bib
new file mode 100644
index 0000000..c9342b1
--- /dev/null
+++ b/references.bib
@@ -0,0 +1,2114 @@
+% Encoding: UTF-8
+@Article{limma,
+ author = {Matthew E Ritchie and Belinda Phipson and Di Wu and Yifang Hu and Charity W Law and Wei Shi and Gordon K Smyth},
+ title = {{limma} powers differential expression analyses for {RNA}-sequencing and microarray studies},
+ journal = {Nucleic Acids Research},
+ year = {2015},
+ volume = {43},
+ number = {7},
+ pages = {e47},
+ doi = {10.1093/nar/gkv007},
+}
+
+@Manual{affyio,
+ title = {affyio: Tools for parsing Affymetrix data files},
+ author = {Ben Bolstad},
+ year = {2019},
+ note = {R package version 1.54.0},
+ url = {https://github.com/bmbolstad/affyio},
+}
+
+@Manual{zeallot,
+ title = {zeallot: Multiple, Unpacking, and Destructuring Assignment},
+ author = {Nathan Teetor},
+ year = {2018},
+ note = {R package version 0.1.0},
+ url = {https://CRAN.R-project.org/package=zeallot},
+}
+
+@Manual{sys,
+ title = {sys: Powerful and Reliable Tools for Running System Commands in R},
+ author = {Jeroen Ooms},
+ year = {2019},
+ note = {R package version 3.3},
+ url = {https://CRAN.R-project.org/package=sys},
+}
+
+@Manual{preprocessCore,
+ title = {preprocessCore: A collection of pre-processing functions},
+ author = {Ben Bolstad},
+ year = {2019},
+ note = {R package version 1.46.0},
+ url = {https://github.com/bmbolstad/preprocessCore},
+}
+
+@Article{vsn,
+ title = {Variance Stabilization Applied to Microarray Data Calibration and to the Quantification of Differential Expression},
+ author = {Wolfgang Huber and Anja {von Heydebreck} and Holger Sueltmann and Annemarie Poustka and Martin Vingron},
+ journal = {Bioinformatics},
+ year = {2002},
+ volume = {18 Suppl. 1},
+ pages = {S96-S104},
+}
+
+@Article{affy,
+ author = {Laurent Gautier and Leslie Cope and Benjamin M. Bolstad and Rafael A. Irizarry},
+ title = {affy---analysis of Affymetrix GeneChip data at the probe level},
+ journal = {Bioinformatics},
+ volume = {20},
+ number = {3},
+ year = {2004},
+ issn = {1367-4803},
+ pages = {307--315},
+ doi = {10.1093/bioinformatics/btg405},
+ publisher = {Oxford University Press},
+ address = {Oxford, UK},
+}
+
+@Manual{impute,
+ title = {impute: impute: Imputation for microarray data},
+ author = {Trevor Hastie and Robert Tibshirani and Balasubramanian Narasimhan and Gilbert Chu},
+ year = {2019},
+ note = {R package version 1.58.0},
+}
+
+@Article{pcaMethods,
+ title = {pcaMethods -- a Bioconductor package providing PCA methods for incomplete data},
+ author = {Wolfram Stacklies and Henning Redestig and Matthias Scholz and Dirk Walther and Joachim Selbig},
+ journal = {Bioinformatics},
+ year = {2007},
+ pages = {1164--1167},
+ volume = {23},
+}
+
+@Manual{mzID,
+ title = {mzID: An mzIdentML parser for R},
+ author = {Thomas Pedersen},
+ year = {2019},
+ note = {R package version 1.22.0},
+}
+
+@Manual{ncdf4,
+ title = {ncdf4: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
+Files},
+ author = {David Pierce},
+ year = {2019},
+ note = {R package version 1.17},
+ url = {https://CRAN.R-project.org/package=ncdf4},
+}
+
+@Manual{Rhdf5lib,
+ title = {Rhdf5lib: hdf5 library as an R package},
+ author = {Mike Smith},
+ year = {2019},
+ note = {R package version 1.6.3},
+}
+
+@Manual{waveslim,
+ title = {waveslim: Basic Wavelet Routines for One-, Two- And Three-Dimensional
+Signal Processing},
+ author = {Brandon Whitcher},
+ year = {2019},
+ note = {R package version 1.7.5.1},
+ url = {https://CRAN.R-project.org/package=waveslim},
+}
+
+@Manual{DEoptimR,
+ title = {DEoptimR: Differential Evolution Optimization in Pure R},
+ author = {Eduardo L. T. Conceicao},
+ year = {2016},
+ note = {R package version 1.0-8},
+ url = {https://CRAN.R-project.org/package=DEoptimR},
+}
+
+@Article{checkmate,
+ title = {{checkmate}: Fast Argument Checks for Defensive R Programming},
+ author = {Michel Lang},
+ journal = {The R Journal},
+ year = {2017},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-028/index.html},
+ pages = {437--445},
+ volume = {9},
+ number = {1},
+}
+
+@Manual{utf8,
+ title = {utf8: Unicode Text Processing},
+ author = {Patrick O. Perry},
+ year = {2018},
+ note = {R package version 1.1.4},
+ url = {https://CRAN.R-project.org/package=utf8},
+}
+
+@Manual{vctrs,
+ title = {vctrs: Vector Helpers},
+ author = {Hadley Wickham and Lionel Henry and Davis Vaughan},
+ year = {2019},
+ note = {R package version 0.2.0},
+ url = {https://CRAN.R-project.org/package=vctrs},
+}
+
+@Manual{formatR,
+ title = {formatR: Format R Code Automatically},
+ author = {Yihui Xie},
+ year = {2019},
+ note = {R package version 1.7},
+ url = {https://CRAN.R-project.org/package=formatR},
+}
+
+@Manual{ini,
+ title = {ini: Read and Write '.ini' Files},
+ author = {David Valentim Dias},
+ year = {2018},
+ note = {R package version 0.3.1},
+ url = {https://CRAN.R-project.org/package=ini},
+}
+
+@Manual{backports,
+ title = {backports: Reimplementations of Functions Introduced Since R-3.0.0},
+ author = {Michel Lang and {R Core Team}},
+ year = {2019},
+ note = {R package version 1.1.5},
+ url = {https://CRAN.R-project.org/package=backports},
+}
+
+@Manual{askpass,
+ title = {askpass: Safe Password Entry for R, Git, and SSH},
+ author = {Jeroen Ooms},
+ year = {2019},
+ note = {R package version 1.1},
+ url = {https://CRAN.R-project.org/package=askpass},
+}
+
+@Manual{e1071,
+ title = {e1071: Misc Functions of the Department of Statistics, Probability
+Theory Group (Formerly: E1071), TU Wien},
+ author = {David Meyer and Evgenia Dimitriadou and Kurt Hornik and Andreas Weingessel and Friedrich Leisch},
+ year = {2019},
+ note = {R package version 1.7-2},
+ url = {https://CRAN.R-project.org/package=e1071},
+}
+
+@Manual{gtools,
+ title = {gtools: Various R Programming Tools},
+ author = {Gregory R. Warnes and Ben Bolker and Thomas Lumley},
+ year = {2018},
+ note = {R package version 3.8.1},
+ url = {https://CRAN.R-project.org/package=gtools},
+}
+
+@Manual{bit,
+ title = {bit: A Class for Vectors of 1-Bit Booleans},
+ author = {Jens Oehlschlagel},
+ year = {2018},
+ note = {R package version 1.1-14},
+ url = {https://CRAN.R-project.org/package=bit},
+}
+
+@Article{MSnbase,
+ title = {MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation},
+ author = {Laurent Gatto and Kathryn Lilley},
+ journal = {Bioinformatics},
+ year = {2012},
+ volume = {28},
+ pages = {288-289},
+}
+
+@Article{mzR1,
+ author = {{Chambers} and Matthew C. and {Maclean} and {Brendan} and {Burke} and {Robert} and {Amodei} and {Dario} and {Ruderman} and Daniel L. and {Neumann} and {Steffen} and {Gatto} and {Laurent} and {Fischer} and {Bernd} and {Pratt} and {Brian} and {Egertson} and {Jarrett} and {Hoff} and {Katherine} and {Kessner} and {Darren} and {Tasman} and {Natalie} and {Shulman} and {Nicholas} and {Frewen} and {Barbara} and {Baker} and Tahmina A. and {Brusniak} and {Mi-Youn} and {Paulse} and {Christopher} and {Creasy} and {David} and {Flashner} and {Lisa} and {Kani} and {Kian} and {Moulding} and {Chris} and {Seymour} and Sean L. and {Nuwaysir} and Lydia M. and {Lefebvre} and {Brent} and {Kuhlmann} and {Frank} and {Roark} and {Joe} and {Rainer} and {Paape} and {Detlev} and {Suckau} and {Hemenway} and {Tina} and {Huhmer} and {Andreas} and {Langridge} and {James} and {Connolly} and {Brian} and {Chadick} and {Trey} and {Holly} and {Krisztina} and {Eckels} and {Josh} and {Deutsch} and Eric W. and {Moritz} and Robert L. and {Katz} and Jonathan E. and {Agus} and David B. and {MacCoss} and {Michael} and {Tabb} and David L. and {Mallick} and {Parag}},
+ year = {2012},
+ journal = {Nat Biotech},
+ title = {{A cross-platform toolkit for mass spectrometry and proteomics}},
+ doi = {10.1038/nbt.2377},
+ pmid = {23051804},
+ month = {oct},
+ number = {10},
+ volume = {30},
+ pages = {918--920},
+ url = {http://dx.doi.org/10.1038/nbt.2377},
+}
+
+@Article{mzR2,
+ author = {Lennart Martens and Matthew Chambers and Marc Sturm and Darren Kessner and Fredrik Levander and Jim Shofstahl and Wilfred H Tang and Andreas Rompp and Steffen Neumann and Angel D Pizarro and Luisa Montecchi-Palazzi and Natalie Tasman and Mike Coleman and Florian Reisinger and Puneet Souda and Henning Hermjakob and Pierre-Alain Binz and Eric W Deutsch},
+ title = {mz{ML} - a {C}ommunity {S}tandard for {M}ass {S}pectrometry {D}ata.},
+ journal = {{Mol Cell Proteomics}},
+ year = {2010},
+ pmid = {20716697},
+ doi = {10.1074/mcp.R110.000133},
+}
+
+@Article{mzR3,
+ author = {Patrick G A Pedrioli and Jimmy K Eng and Robert Hubley and Mathijs Vogelzang and Eric W Deutsch and Brian Raught and Brian Pratt and Erik Nilsson and Ruth H Angeletti and Rolf Apweiler and Kei Cheung and Catherine E Costello and Henning Hermjakob and Sequin Huang and Randall K Julian and Eugene Kapp and Mark E McComb and Stephen G Oliver and Gilbert Omenn and Norman W Paton and Richard Simpson and Richard Smith and Chris F Taylor and Weimin Zhu and Ruedi Aebersold},
+ title = {{A} common open representation of mass spectrometry data and its
+ application to proteomics research.},
+ journal = {Nat Biotechnol},
+ year = {2004},
+ volume = {22},
+ number = {11},
+ pages = {{1459--1466}},
+ pmid = {15529173},
+ doi = {10.1038/nbt1031},
+}
+
+@Article{mzR4,
+ author = {Andrew Keller and Jimmy Eng and Ning Zhang and Xiao-jun Li and Ruedi Aebersold},
+ title = {{A} uniform proteomics {MS}/{MS} analysis platform utilizing open {XML} file formats.},
+ journal = {Mol Syst Biol},
+ year = {2005},
+}
+
+@Article{mzR5,
+ author = {Darren Kessner and Matt Chambers and Robert Burke and David Agus and Parag Mallick},
+ title = {{P}roteo{W}izard: open source software for rapid proteomics tools
+ development.},
+ journal = {Bioinformatics},
+ year = {2008},
+ volume = {24},
+ number = {21},
+ pages = {2534--2536},
+ doi = {10.1093/bioinformatics/btn323},
+ pmid = {18606607},
+}
+
+@Article{plyr,
+ title = {The Split-Apply-Combine Strategy for Data Analysis},
+ author = {Hadley Wickham},
+ journal = {Journal of Statistical Software},
+ year = {2011},
+ volume = {40},
+ number = {1},
+ pages = {1--29},
+ url = {http://www.jstatsoft.org/v40/i01/},
+}
+
+@Manual{RANN,
+ title = {RANN: Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
+Metric},
+ author = {Sunil Arya and David Mount and Samuel E. Kemp and Gregory Jefferis},
+ year = {2019},
+ note = {R package version 2.6.1},
+ url = {https://CRAN.R-project.org/package=RANN},
+}
+
+@Article{MassSpecWavelet,
+ author = {Pan Du and Warren A. Kibbe and Simon M. Lin},
+ title = {Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching},
+ journal = {Bioinformatics},
+ year = {2006},
+ volume = {22},
+ pages = {2059-2065},
+}
+
+@Manual{robustbase1,
+ title = {robustbase: Basic Robust Statistics},
+ author = {Martin Maechler and Peter Rousseeuw and Christophe Croux and Valentin Todorov and Andreas Ruckstuhl and Matias Salibian-Barrera and Tobias Verbeke and Manuel Koller and Eduardo L. T. Conceicao and Maria {Anna di Palma}},
+ year = {2019},
+ note = {R package version 0.93-5},
+ url = {http://robustbase.r-forge.r-project.org/},
+ url = {http://robustbase.r-forge.r-project.org/},
+}
+
+@Article{robustbase2,
+ title = {An Object-Oriented Framework for Robust Multivariate Analysis},
+ author = {Valentin Todorov and Peter Filzmoser},
+ journal = {Journal of Statistical Software},
+ year = {2009},
+ volume = {32},
+ number = {3},
+ pages = {1--47},
+ url = {http://www.jstatsoft.org/v32/i03/},
+}
+
+@Article{Formula,
+ title = {Extended Model Formulas in {R}: Multiple Parts and Multiple Responses},
+ author = {Achim Zeileis and Yves Croissant},
+ journal = {Journal of Statistical Software},
+ year = {2010},
+ volume = {34},
+ number = {1},
+ pages = {1--13},
+ doi = {10.18637/jss.v034.i01},
+}
+
+@Manual{latticeExtra,
+ title = {latticeExtra: Extra Graphical Utilities Based on Lattice},
+ author = {Deepayan Sarkar and Felix Andrews},
+ year = {2016},
+ note = {R package version 0.6-28},
+ url = {https://CRAN.R-project.org/package=latticeExtra},
+}
+
+@Manual{acepack,
+ title = {acepack: ACE and AVAS for Selecting Multiple Regression Transformations},
+ author = {Phil Spector and Jerome Friedman and Robert Tibshirani and Thomas Lumley and Shawn Garbett and Jonathan Baron},
+ year = {2016},
+ note = {R package version 1.4.1},
+ url = {https://CRAN.R-project.org/package=acepack},
+}
+
+@Manual{htmlTable,
+ title = {htmlTable: Advanced Tables for Markdown/HTML},
+ author = {Max Gordon and Stephen Gragg and Peter Konings},
+ year = {2019},
+ note = {R package version 1.13.2},
+ url = {https://CRAN.R-project.org/package=htmlTable},
+}
+
+@Manual{viridis,
+ title = {viridis: Default Color Maps from 'matplotlib'},
+ author = {Simon Garnier},
+ year = {2018},
+ note = {R package version 0.5.1},
+ url = {https://CRAN.R-project.org/package=viridis},
+}
+
+@Manual{base64enc,
+ title = {base64enc: Tools for base64 encoding},
+ author = {Simon Urbanek},
+ year = {2015},
+ note = {R package version 0.1-3},
+ url = {https://CRAN.R-project.org/package=base64enc},
+}
+
+@Manual{labeling,
+ title = {labeling: Axis Labeling},
+ author = {Justin Talbot},
+ year = {2014},
+ note = {R package version 0.3},
+ url = {https://CRAN.R-project.org/package=labeling},
+}
+
+@Manual{munsell,
+ title = {munsell: Utilities for Using Munsell Colours},
+ author = {Charlotte Wickham},
+ year = {2018},
+ note = {R package version 0.5.0},
+ url = {https://CRAN.R-project.org/package=munsell},
+}
+
+@Manual{fansi,
+ title = {fansi: ANSI Control Sequence Aware String Functions},
+ author = {Brodie Gaslam},
+ year = {2018},
+ note = {R package version 0.4.0},
+ url = {https://CRAN.R-project.org/package=fansi},
+}
+
+@Manual{pillar,
+ title = {pillar: Coloured Formatting for Columns},
+ author = {Kirill Muller and Hadley Wickham},
+ year = {2019},
+ note = {R package version 1.4.2},
+ url = {https://CRAN.R-project.org/package=pillar},
+}
+
+@Manual{biglm,
+ title = {biglm: bounded memory linear and generalized linear models},
+ author = {Thomas Lumley},
+ year = {2013},
+ note = {R package version 0.9-1},
+ url = {https://CRAN.R-project.org/package=biglm},
+}
+
+@Manual{yaml,
+ title = {yaml: Methods to Convert R Data to YAML and Back},
+ author = {Jeremy Stephens and Kirill Simonov and Yihui Xie and Zhuoer Dong and Hadley Wickham and Jeffrey Horner and {reikoch} and Will Beasley and Brendan O'Connor and Gregory R. Warnes},
+ year = {2018},
+ note = {R package version 2.2.0},
+ url = {https://CRAN.R-project.org/package=yaml},
+}
+
+@Manual{bitops,
+ title = {bitops: Bitwise Operations},
+ author = {S original by Steve Dutky initial R port and extensions by Martin Maechler; revised and modified by Steve Dutky},
+ year = {2013},
+ note = {R package version 1.0-6},
+ url = {https://CRAN.R-project.org/package=bitops},
+}
+
+@Manual{lambda.r,
+ title = {lambda.r: Modeling Data with Functional Programming},
+ author = {Brian Lee Yung Rowe},
+ year = {2019},
+ note = {R package version 1.2.4},
+ url = {https://CRAN.R-project.org/package=lambda.r},
+}
+
+@Manual{futile.options,
+ title = {futile.options: Futile Options Management},
+ author = {Brian Lee Yung Rowe},
+ year = {2018},
+ note = {R package version 1.0.1},
+ url = {https://CRAN.R-project.org/package=futile.options},
+}
+
+@Manual{clipr,
+ title = {clipr: Read and Write from the System Clipboard},
+ author = {Matthew Lincoln},
+ year = {2019},
+ note = {R package version 0.7.0},
+ url = {https://CRAN.R-project.org/package=clipr},
+}
+
+@Manual{clisymbols,
+ title = {clisymbols: Unicode Symbols at the R Prompt},
+ author = {Gabor Csardi and Sindre Sorhus},
+ year = {2017},
+ note = {R package version 1.2.0},
+ url = {https://CRAN.R-project.org/package=clisymbols},
+}
+
+@Manual{gh,
+ title = {gh: 'GitHub' 'API'},
+ author = {Jennifer Bryan and Hadley Wickham},
+ year = {2017},
+ note = {R package version 1.0.1},
+ url = {https://CRAN.R-project.org/package=gh},
+}
+
+@Manual{rprojroot,
+ title = {rprojroot: Finding Files in Project Subdirectories},
+ author = {Kirill Muller},
+ year = {2018},
+ note = {R package version 1.3-2},
+ url = {https://CRAN.R-project.org/package=rprojroot},
+}
+
+@Manual{whisker,
+ title = {whisker: {{mustache}} for R, Logicless Templating},
+ author = {Edwin {de Jonge}},
+ year = {2019},
+ note = {R package version 0.4},
+ url = {https://CRAN.R-project.org/package=whisker},
+}
+
+@Manual{rex,
+ title = {rex: Friendly Regular Expressions},
+ author = {Kevin Ushey and Jim Hester and Robert Krzyzanowski},
+ year = {2017},
+ note = {R package version 1.1.2},
+ url = {https://CRAN.R-project.org/package=rex},
+}
+
+@Manual{promises,
+ title = {promises: Abstractions for Promise-Based Asynchronous Programming},
+ author = {Joe Cheng},
+ year = {2019},
+ note = {R package version 1.1.0},
+ url = {https://CRAN.R-project.org/package=promises},
+}
+
+@Manual{mime,
+ title = {mime: Map Filenames to MIME Types},
+ author = {Yihui Xie},
+ year = {2019},
+ note = {R package version 0.7},
+ url = {https://CRAN.R-project.org/package=mime},
+}
+
+@Manual{openssl,
+ title = {openssl: Toolkit for Encryption, Signatures and Certificates Based on
+OpenSSL},
+ author = {Jeroen Ooms},
+ year = {2019},
+ note = {R package version 1.4.1},
+ url = {https://CRAN.R-project.org/package=openssl},
+}
+
+@Manual{prettyunits,
+ title = {prettyunits: Pretty, Human Readable Formatting of Quantities},
+ author = {Gabor Csardi},
+ year = {2015},
+ note = {R package version 1.0.2},
+ url = {https://CRAN.R-project.org/package=prettyunits},
+}
+
+@Manual{xopen,
+ title = {xopen: Open System Files, 'URLs', Anything},
+ author = {Gabor Csardi and Fathi Boudra and Rex Dieter and Kevin Krammer and Jeremy White},
+ year = {2018},
+ note = {R package version 1.0.0},
+ url = {https://CRAN.R-project.org/package=xopen},
+}
+
+@Manual{brew,
+ title = {brew: Templating Framework for Report Generation},
+ author = {Jeffrey Horner},
+ year = {2011},
+ note = {R package version 1.0-6},
+ url = {https://CRAN.R-project.org/package=brew},
+}
+
+@Manual{commonmark,
+ title = {commonmark: High Performance CommonMark and Github Markdown Rendering in R},
+ author = {Jeroen Ooms},
+ year = {2018},
+ note = {R package version 1.7},
+ url = {https://CRAN.R-project.org/package=commonmark},
+}
+
+@Manual{xml2,
+ title = {xml2: Parse XML},
+ author = {Hadley Wickham and Jim Hester and Jeroen Ooms},
+ year = {2019},
+ note = {R package version 1.2.2},
+ url = {https://CRAN.R-project.org/package=xml2},
+}
+
+@Manual{evaluate,
+ title = {evaluate: Parsing and Evaluation Tools that Provide More Details than the
+Default},
+ author = {Hadley Wickham and Yihui Xie},
+ year = {2019},
+ note = {R package version 0.14},
+ url = {https://CRAN.R-project.org/package=evaluate},
+}
+
+@Manual{praise,
+ title = {praise: Praise Users},
+ author = {Gabor Csardi and Sindre Sorhus},
+ year = {2015},
+ note = {R package version 1.0.0},
+ url = {https://CRAN.R-project.org/package=praise},
+}
+
+@Manual{classInt,
+ title = {classInt: Choose Univariate Class Intervals},
+ author = {Roger Bivand},
+ year = {2019},
+ note = {R package version 0.4-2},
+ url = {https://CRAN.R-project.org/package=classInt},
+}
+
+@Manual{DBI,
+ title = {DBI: R Database Interface},
+ author = {{R Special Interest Group on Databases (R-SIG-DB)} and Hadley Wickham and Kirill Muller},
+ year = {2018},
+ note = {R package version 1.0.0},
+ url = {https://CRAN.R-project.org/package=DBI},
+}
+
+@Article{units,
+ title = {Measurement Units in {R}},
+ author = {Edzer Pebesma and Thomas Mailund and James Hiebert},
+ year = {2016},
+ journal = {R Journal},
+ doi = {10.32614/RJ-2016-061},
+ pages = {486--494},
+ volume = {8},
+ number = {2},
+}
+
+@Manual{gdata,
+ title = {gdata: Various R Programming Tools for Data Manipulation},
+ author = {Gregory R. Warnes and Ben Bolker and Gregor Gorjanc and Gabor Grothendieck and Ales Korosec and Thomas Lumley and Don MacQueen and Arni Magnusson and Jim Rogers and others},
+ year = {2017},
+ note = {R package version 2.18.0},
+ url = {https://CRAN.R-project.org/package=gdata},
+}
+
+@Manual{highr,
+ title = {highr: Syntax Highlighting for R Source Code},
+ author = {Yixuan Qiu and Yihui Xie},
+ year = {2019},
+ note = {R package version 0.8},
+ url = {https://CRAN.R-project.org/package=highr},
+}
+
+@Manual{markdown,
+ title = {markdown: Render Markdown with the C Library 'Sundown'},
+ author = {JJ Allaire and Jeffrey Horner and Yihui Xie and Vicent Marti and Natacha Porte},
+ year = {2019},
+ note = {R package version 1.1},
+ url = {https://CRAN.R-project.org/package=markdown},
+}
+
+@Manual{xfun,
+ title = {xfun: Miscellaneous Functions by 'Yihui Xie'},
+ author = {Yihui Xie},
+ year = {2019},
+ note = {R package version 0.10},
+ url = {https://CRAN.R-project.org/package=xfun},
+}
+
+@Manual{httpuv,
+ title = {httpuv: HTTP and WebSocket Server Library},
+ author = {Joe Cheng and Hector Corrada Bravo and Jeroen Ooms and Winston Chang},
+ year = {2019},
+ note = {R package version 1.5.2},
+ url = {https://CRAN.R-project.org/package=httpuv},
+}
+
+@Manual{xtable,
+ title = {xtable: Export Tables to LaTeX or HTML},
+ author = {David B. Dahl and David Scott and Charles Roosen and Arni Magnusson and Jonathan Swinton},
+ year = {2019},
+ note = {R package version 1.8-4},
+ url = {https://CRAN.R-project.org/package=xtable},
+}
+
+@Manual{sourcetools,
+ title = {sourcetools: Tools for Reading, Tokenizing and Parsing R Code},
+ author = {Kevin Ushey},
+ year = {2018},
+ note = {R package version 0.1.7},
+ url = {https://CRAN.R-project.org/package=sourcetools},
+}
+
+@Manual{later,
+ title = {later: Utilities for Scheduling Functions to Execute Later with Event
+Loops},
+ author = {Joe Cheng and Winston Chang},
+ year = {2019},
+ note = {R package version 1.0.0},
+ url = {https://CRAN.R-project.org/package=later},
+}
+
+@Manual{fastmap,
+ title = {fastmap: Fast Implementation of a Key-Value Store},
+ author = {Winston Chang},
+ year = {2019},
+ note = {R package version 1.0.1},
+ url = {https://CRAN.R-project.org/package=fastmap},
+}
+
+@Manual{miniUI,
+ title = {miniUI: Shiny UI Widgets for Small Screens},
+ author = {Joe Cheng},
+ year = {2018},
+ note = {R package version 0.1.1.1},
+ url = {https://CRAN.R-project.org/package=miniUI},
+}
+
+@Manual{webshot,
+ title = {webshot: Take Screenshots of Web Pages},
+ author = {Winston Chang},
+ year = {2018},
+ note = {R package version 0.5.1},
+ url = {https://CRAN.R-project.org/package=webshot},
+}
+
+@Manual{bit64,
+ title = {bit64: A S3 Class for Vectors of 64bit Integers},
+ author = {Jens Oehlschlagel},
+ year = {2017},
+ note = {R package version 0.9-7},
+ url = {https://CRAN.R-project.org/package=bit64},
+}
+
+@Manual{blob,
+ title = {blob: A Simple S3 Class for Representing Vectors of Binary Data
+('BLOBS')},
+ author = {Hadley Wickham},
+ year = {2019},
+ note = {R package version 1.2.0},
+ url = {https://CRAN.R-project.org/package=blob},
+}
+
+@Manual{dbplyr,
+ title = {dbplyr: A 'dplyr' Back End for Databases},
+ author = {Hadley Wickham and Edgar Ruiz},
+ year = {2019},
+ note = {R package version 1.4.2},
+ url = {https://CRAN.R-project.org/package=dbplyr},
+}
+
+@Article{Biobase,
+ author = {W. Huber and V. J. Carey and R. Gentleman and S. Anders and M. Carlson and B. S. Carvalho and H. C. Bravo and S. Davis and L. Gatto and T. Girke and R. Gottardo and F. Hahne and K. D. Hansen and R. A. Irizarry and M. Lawrence and M. I. Love and J. MacDonald and V. Obenchain and A. K. {Ole's} and H. {Pag`es} and A. Reyes and P. Shannon and G. K. Smyth and D. Tenenbaum and L. Waldron and M. Morgan},
+ title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
+ journal = {Nature Methods},
+ year = {2015},
+ volume = {12},
+ number = {2},
+ pages = {115--121},
+ url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
+}
+
+@Article{xcms1,
+ author = {{Smith} and {C.A.} and {Want} and {E.J.} and {O'Maille} and {G.} and {Abagyan,R.} and {Siuzdak} and {G.}},
+ title = {XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification},
+ journal = {Analytical Chemistry},
+ year = {2006},
+ volume = {78},
+ pages = {779--787},
+}
+
+@Article{xcms2,
+ author = {Ralf Tautenhahn and Christoph Boettcher and Steffen Neumann},
+ title = {Highly sensitive feature detection for high resolution LC/MS},
+ journal = {BMC Bioinformatics},
+ year = {2008},
+ volume = {9},
+ pages = {504},
+}
+
+@Article{xcms3,
+ author = {H. Paul Benton and Elizabeth J. Want and Timothy M. D. Ebbels},
+ title = {Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data},
+ journal = {BIOINFORMATICS},
+ year = {2010},
+ volume = {26},
+ pages = {2488},
+}
+
+@Manual{RBGL,
+ title = {RBGL: An interface to the BOOST graph library},
+ author = {Vince Carey and Li Long and R. Gentleman},
+ year = {2019},
+ note = {R package version 1.60.0},
+ url = {http://www.bioconductor.org},
+}
+
+@Manual{graph,
+ title = {graph: graph: A package to handle graph data structures},
+ author = {R. Gentleman and Elizabeth Whalen and W. Huber and S. Falcon},
+ year = {2019},
+ note = {R package version 1.62.0},
+}
+
+@Manual{Hmisc,
+ title = {Hmisc: Harrell Miscellaneous},
+ author = {Frank E {Harrell Jr} and with contributions from Charles Dupont and many others.},
+ year = {2019},
+ note = {R package version 4.3-0},
+ url = {https://CRAN.R-project.org/package=Hmisc},
+}
+
+@Manual{remotes,
+ title = {remotes: R Package Installation from Remote Repositories, Including
+'GitHub'},
+ author = {Jim Hester and Gabor Csardi and Hadley Wickham and Winston Chang and Martin Morgan and Dan Tenenbaum},
+ year = {2019},
+ note = {R package version 2.1.0},
+ url = {https://CRAN.R-project.org/package=remotes},
+}
+
+@Manual{magrittr,
+ title = {magrittr: A Forward-Pipe Operator for R},
+ author = {Stefan Milton Bache and Hadley Wickham},
+ year = {2014},
+ note = {R package version 1.5},
+ url = {https://CRAN.R-project.org/package=magrittr},
+}
+
+@Manual{rlang,
+ title = {rlang: Functions for Base Types and Core R and 'Tidyverse' Features},
+ author = {Lionel Henry and Hadley Wickham},
+ year = {2019},
+ note = {R package version 0.4.0},
+ url = {https://CRAN.R-project.org/package=rlang},
+}
+
+@Manual{curl,
+ title = {curl: A Modern and Flexible Web Client for R},
+ author = {Jeroen Ooms},
+ year = {2019},
+ note = {R package version 4.2},
+ url = {https://CRAN.R-project.org/package=curl},
+}
+
+@Manual{digest,
+ title = {digest: Create Compact Hash Digests of R Objects},
+ author = {Dirk Eddelbuettel with contributions by Antoine Lucas and Jarek Tuszynski and Henrik Bengtsson and Simon Urbanek and Mario Frasca and Bryan Lewis and Murray Stokely and Hannes Muehleisen and Duncan Murdoch and Jim Hester and Wush Wu and Qiang Kou and Thierry Onkelinx and Michel Lang and Viliam Simko and Kurt Hornik and Radford Neal and Kendon Bell and and Matthew {de Queljoe.}},
+ year = {2019},
+ note = {R package version 0.6.21},
+ url = {https://CRAN.R-project.org/package=digest},
+}
+
+@Manual{lazyeval,
+ title = {lazyeval: Lazy (Non-Standard) Evaluation},
+ author = {Hadley Wickham},
+ year = {2019},
+ note = {R package version 0.2.2},
+ url = {https://CRAN.R-project.org/package=lazyeval},
+}
+
+@Article{reshape2,
+ title = {Reshaping Data with the {reshape} Package},
+ author = {Hadley Wickham},
+ journal = {Journal of Statistical Software},
+ year = {2007},
+ volume = {21},
+ number = {12},
+ pages = {1--20},
+ url = {http://www.jstatsoft.org/v21/i12/},
+}
+
+@Manual{scales,
+ title = {scales: Scale Functions for Visualization},
+ author = {Hadley Wickham},
+ year = {2018},
+ note = {R package version 1.0.0},
+ url = {https://CRAN.R-project.org/package=scales},
+}
+
+@Manual{tibble,
+ title = {tibble: Simple Data Frames},
+ author = {Kirill Muller and Hadley Wickham},
+ year = {2019},
+ note = {R package version 2.1.3},
+ url = {https://CRAN.R-project.org/package=tibble},
+}
+
+@Manual{viridisLite,
+ title = {viridisLite: Default Color Maps from 'matplotlib' (Lite Version)},
+ author = {Simon Garnier},
+ year = {2018},
+ note = {R package version 0.3.0},
+ url = {https://CRAN.R-project.org/package=viridisLite},
+}
+
+@Manual{withr,
+ title = {withr: Run Code 'With' Temporarily Modified Global State},
+ author = {Jim Hester and Kirill Muller and Kevin Ushey and Hadley Wickham and Winston Chang},
+ year = {2018},
+ note = {R package version 2.1.2},
+ url = {https://CRAN.R-project.org/package=withr},
+}
+
+@Article{jsonlite,
+ title = {The jsonlite Package: A Practical and Consistent Mapping Between JSON Data and R Objects},
+ author = {Jeroen Ooms},
+ journal = {arXiv:1403.2805 [stat.CO]},
+ year = {2014},
+ url = {https://arxiv.org/abs/1403.2805},
+}
+
+@Manual{assertthat,
+ title = {assertthat: Easy Pre and Post Assertions},
+ author = {Hadley Wickham},
+ year = {2019},
+ note = {R package version 0.2.1},
+ url = {https://CRAN.R-project.org/package=assertthat},
+}
+
+@Manual{glue,
+ title = {glue: Interpreted String Literals},
+ author = {Jim Hester},
+ year = {2019},
+ note = {R package version 1.3.1},
+ url = {https://CRAN.R-project.org/package=glue},
+}
+
+@Manual{pkgconfig,
+ title = {pkgconfig: Private Configuration for 'R' Packages},
+ author = {Gabor Csardi},
+ year = {2019},
+ note = {R package version 2.0.3},
+ url = {https://CRAN.R-project.org/package=pkgconfig},
+}
+
+@Manual{R6,
+ title = {R6: Encapsulated Classes with Reference Semantics},
+ author = {Winston Chang},
+ year = {2019},
+ note = {R package version 2.4.0},
+ url = {https://CRAN.R-project.org/package=R6},
+}
+
+@Manual{tidyselect,
+ title = {tidyselect: Select from a Set of Strings},
+ author = {Lionel Henry and Hadley Wickham},
+ year = {2018},
+ note = {R package version 0.2.5},
+ url = {https://CRAN.R-project.org/package=tidyselect},
+}
+
+@Manual{BH,
+ title = {BH: Boost C++ Header Files},
+ author = {Dirk Eddelbuettel and John W. Emerson and Michael J. Kane},
+ year = {2019},
+ note = {R package version 1.69.0-1},
+ url = {https://CRAN.R-project.org/package=BH},
+}
+
+@Manual{plogr,
+ title = {plogr: The 'plog' C++ Logging Library},
+ author = {Kirill Muller},
+ year = {2018},
+ note = {R package version 0.2.0},
+ url = {https://CRAN.R-project.org/package=plogr},
+}
+
+@Manual{stringi,
+ title = {R package stringi: Character string processing facilities},
+ author = {Marek Gagolewski},
+ year = {2019},
+ url = {http://www.gagolewski.com/software/stringi/},
+}
+
+@Manual{zlibbioc,
+ title = {zlibbioc: An R packaged zlib-1.2.5},
+ author = {Martin Morgan},
+ year = {2019},
+ note = {R package version 1.30.0},
+ url = {http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html},
+}
+
+@Manual{irlba,
+ title = {irlba: Fast Truncated Singular Value Decomposition and Principal
+Components Analysis for Large Dense and Sparse Matrices},
+ author = {Jim Baglama and Lothar Reichel and B. W. Lewis},
+ year = {2019},
+ note = {R package version 2.3.3},
+ url = {https://CRAN.R-project.org/package=irlba},
+}
+
+@Manual{matter,
+ title = {matter: A framework for rapid prototyping with binary data on disk},
+ author = {Kylie A. Bemis},
+ year = {2019},
+ note = {R package version 1.10.0},
+ url = {https://github.com/kuwisdelu/matter},
+}
+
+@Article{mclust,
+ title = {{mclust} 5: clustering, classification and density estimation using {G}aussian finite mixture models},
+ author = {Luca Scrucca and Michael Fop and Thomas Brendan Murphy and Adrian E. Raftery},
+ journal = {The {R} Journal},
+ year = {2016},
+ volume = {8},
+ number = {1},
+ pages = {205--233},
+ url = {https://journal.r-project.org/archive/2016-1/scrucca-fop-murphy-etal.pdf},
+}
+
+@Manual{signal,
+ title = {{signal}: Signal processing},
+ author = {{signal developers}},
+ year = {2014},
+ url = {http://r-forge.r-project.org/projects/signal/},
+}
+
+@Article{sp1,
+ author = {Edzer J. Pebesma and Roger S. Bivand},
+ title = {Classes and methods for spatial data in {R}},
+ journal = {R News},
+ year = {2005},
+ volume = {5},
+ number = {2},
+ pages = {9--13},
+ month = {November},
+ url = {https://CRAN.R-project.org/doc/Rnews/},
+}
+
+@Book{sp2,
+ author = {Roger S. Bivand and Edzer Pebesma and Virgilio Gomez-Rubio},
+ title = {Applied spatial data analysis with {R}, Second edition},
+ year = {2013},
+ publisher = {Springer, NY},
+ url = {http://www.asdar-book.org/},
+}
+
+@Manual{abind,
+ title = {abind: Combine Multidimensional Arrays},
+ author = {Tony Plate and Richard Heiberger},
+ year = {2016},
+ note = {R package version 1.4-5},
+ url = {https://CRAN.R-project.org/package=abind},
+}
+
+@Manual{tiff,
+ title = {tiff: Read and write TIFF images},
+ author = {Simon Urbanek},
+ year = {2013},
+ note = {R package version 0.1-5},
+ url = {https://CRAN.R-project.org/package=tiff},
+}
+
+@Manual{jpeg,
+ title = {jpeg: Read and write JPEG images},
+ author = {Simon Urbanek},
+ year = {2014},
+ note = {R package version 0.1-8},
+ url = {https://CRAN.R-project.org/package=jpeg},
+}
+
+@Manual{png,
+ title = {png: Read and write PNG images},
+ author = {Simon Urbanek},
+ year = {2013},
+ note = {R package version 0.1-7},
+ url = {https://CRAN.R-project.org/package=png},
+}
+
+@Manual{locfit,
+ title = {locfit: Local Regression, Likelihood and Density Estimation.},
+ author = {Catherine Loader},
+ year = {2013},
+ note = {R package version 1.5-9.1},
+ url = {https://CRAN.R-project.org/package=locfit},
+}
+
+@Manual{fftwtools,
+ title = {fftwtools: Wrapper for 'FFTW3' Includes: One-Dimensional Univariate,
+One-Dimensional Multivariate, and Two-Dimensional Transform},
+ author = {Karim Rahim},
+ year = {2017},
+ note = {R package version 0.9-8},
+ url = {https://CRAN.R-project.org/package=fftwtools},
+}
+
+@Manual{htmltools,
+ title = {htmltools: Tools for HTML},
+ author = {{RStudio} and {Inc.}},
+ year = {2019},
+ note = {R package version 0.4.0},
+ url = {https://CRAN.R-project.org/package=htmltools},
+}
+
+@Manual{htmlwidgets,
+ title = {htmlwidgets: HTML Widgets for R},
+ author = {Ramnath Vaidyanathan and Yihui Xie and JJ Allaire and Joe Cheng and Kenton Russell},
+ year = {2019},
+ note = {R package version 1.5.1},
+ url = {https://CRAN.R-project.org/package=htmlwidgets},
+}
+
+@Manual{RCurl,
+ title = {RCurl: General Network (HTTP/FTP/...) Client Interface for R},
+ author = {Duncan Temple Lang and the CRAN team},
+ year = {2019},
+ note = {R package version 1.95-4.12},
+ url = {https://CRAN.R-project.org/package=RCurl},
+}
+
+@Manual{futile.logger,
+ title = {futile.logger: A Logging Utility for R},
+ author = {Brian Lee Yung Rowe},
+ year = {2016},
+ note = {R package version 1.4.3},
+ url = {https://CRAN.R-project.org/package=futile.logger},
+}
+
+@Manual{snow,
+ title = {snow: Simple Network of Workstations},
+ author = {Luke Tierney and A. J. Rossini and Na Li and H. Sevcikova},
+ year = {2018},
+ note = {R package version 0.4-3},
+ url = {https://CRAN.R-project.org/package=snow},
+}
+
+@Manual{tools,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{compiler,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{usethis,
+ title = {usethis: Automate Package and Project Setup},
+ author = {Hadley Wickham and Jennifer Bryan},
+ year = {2019},
+ note = {R package version 1.5.1},
+ url = {https://CRAN.R-project.org/package=usethis},
+}
+
+@Manual{callr,
+ title = {callr: Call R from R},
+ author = {Gabor Csardi and Winston Chang},
+ year = {2019},
+ note = {R package version 3.3.2},
+ url = {https://CRAN.R-project.org/package=callr},
+}
+
+@Manual{cli,
+ title = {cli: Helpers for Developing Command Line Interfaces},
+ author = {Gabor Csardi},
+ year = {2019},
+ note = {R package version 1.1.0},
+ url = {https://CRAN.R-project.org/package=cli},
+}
+
+@Manual{covr,
+ title = {covr: Test Coverage for Packages},
+ author = {Jim Hester},
+ year = {2019},
+ note = {R package version 3.3.2},
+ url = {https://CRAN.R-project.org/package=covr},
+}
+
+@Manual{crayon,
+ title = {crayon: Colored Terminal Output},
+ author = {Gabor Csardi},
+ year = {2017},
+ note = {R package version 1.3.4},
+ url = {https://CRAN.R-project.org/package=crayon},
+}
+
+@Manual{desc,
+ title = {desc: Manipulate DESCRIPTION Files},
+ author = {Gabor Csardi and Kirill Muller and Jim Hester},
+ year = {2018},
+ note = {R package version 1.2.0},
+ url = {https://CRAN.R-project.org/package=desc},
+}
+
+@Manual{DT,
+ title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
+ author = {Yihui Xie and Joe Cheng and Xianying Tan},
+ year = {2019},
+ note = {R package version 0.9},
+ url = {https://CRAN.R-project.org/package=DT},
+}
+
+@Manual{ellipsis,
+ title = {ellipsis: Tools for Working with ...},
+ author = {Hadley Wickham},
+ year = {2019},
+ note = {R package version 0.3.0},
+ url = {https://CRAN.R-project.org/package=ellipsis},
+}
+
+@Manual{git2r,
+ author = {Stefan Widgren and others},
+ title = {{git2r}: Provides Access to Git Repositories},
+ year = {2018},
+ note = {R package version 0.21.0},
+ url = {https://CRAN.R-project.org/package=git2r},
+}
+
+@Manual{httr,
+ title = {httr: Tools for Working with URLs and HTTP},
+ author = {Hadley Wickham},
+ year = {2019},
+ note = {R package version 1.4.1},
+ url = {https://CRAN.R-project.org/package=httr},
+}
+
+@Manual{memoise,
+ title = {memoise: Memoisation of Functions},
+ author = {Hadley Wickham and Jim Hester and Kirill Muller and Daniel Cook},
+ year = {2017},
+ note = {R package version 1.1.0},
+ url = {https://CRAN.R-project.org/package=memoise},
+}
+
+@Manual{pkgbuild,
+ title = {pkgbuild: Find Tools Needed to Build R Packages},
+ author = {Hadley Wickham and Jim Hester},
+ year = {2019},
+ note = {R package version 1.0.6},
+ url = {https://CRAN.R-project.org/package=pkgbuild},
+}
+
+@Manual{pkgload,
+ title = {pkgload: Simulate Package Installation and Attach},
+ author = {Hadley Wickham and Jim Hester and Winston Chang},
+ year = {2018},
+ note = {R package version 1.0.2},
+ url = {https://CRAN.R-project.org/package=pkgload},
+}
+
+@Manual{rcmdcheck,
+ title = {rcmdcheck: Run 'R CMD check' from 'R' and Capture Results},
+ author = {Gabor Csardi},
+ year = {2019},
+ note = {R package version 1.3.3},
+ url = {https://CRAN.R-project.org/package=rcmdcheck},
+}
+
+@Manual{roxygen2,
+ title = {roxygen2: In-Line Documentation for R},
+ author = {Hadley Wickham and Peter Danenberg and Manuel Eugster},
+ year = {2018},
+ note = {R package version 6.1.1},
+ url = {https://CRAN.R-project.org/package=roxygen2},
+}
+
+@Manual{rstudioapi,
+ title = {rstudioapi: Safely Access the RStudio API},
+ author = {Kevin Ushey and JJ Allaire and Hadley Wickham and Gary Ritchie},
+ year = {2019},
+ note = {R package version 0.10},
+ url = {https://CRAN.R-project.org/package=rstudioapi},
+}
+
+@Manual{rversions,
+ title = {rversions: Query 'R' Versions, Including 'r-release' and 'r-oldrel'},
+ author = {Gabor Csardi},
+ year = {2019},
+ note = {R package version 2.0.0},
+ url = {https://CRAN.R-project.org/package=rversions},
+}
+
+@Manual{sessioninfo,
+ title = {sessioninfo: R Session Information},
+ author = {Gabor Csardi and R core and Hadley Wickham and Winston Chang and Robert M Flight and Kirill Muller and Jim Hester},
+ year = {2018},
+ note = {R package version 1.1.1},
+ url = {https://CRAN.R-project.org/package=sessioninfo},
+}
+
+@Article{testthat,
+ author = {Hadley Wickham},
+ title = {testthat: Get Started with Testing},
+ journal = {The R Journal},
+ year = {2011},
+ volume = {3},
+ pages = {5--10},
+ url = {https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf},
+}
+
+@Manual{ps,
+ title = {ps: List, Query, Manipulate System Processes},
+ author = {Jay Loden and Dave Daeschler and Giampaolo Rodola' and Gabor Csardi},
+ year = {2018},
+ note = {R package version 1.3.0},
+ url = {https://CRAN.R-project.org/package=ps},
+}
+
+@Manual{spData,
+ title = {spData: Datasets for Spatial Analysis},
+ author = {Roger Bivand and Jakub Nowosad and Robin Lovelace},
+ year = {2019},
+ note = {R package version 0.3.2},
+ url = {https://CRAN.R-project.org/package=spData},
+}
+
+@Article{sf,
+ author = {Edzer Pebesma},
+ title = {{Simple Features for R: Standardized Support for Spatial Vector Data}},
+ year = {2018},
+ journal = {{The R Journal}},
+ doi = {10.32614/RJ-2018-009},
+ url = {https://doi.org/10.32614/RJ-2018-009},
+ pages = {439--446},
+ volume = {10},
+ number = {1},
+}
+
+@Manual{deldir,
+ title = {deldir: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation},
+ author = {Rolf Turner},
+ year = {2019},
+ note = {R package version 0.1-23},
+ url = {https://CRAN.R-project.org/package=deldir},
+}
+
+@Manual{LearnBayes,
+ title = {LearnBayes: Functions for Learning Bayesian Inference},
+ author = {Jim Albert},
+ year = {2018},
+ note = {R package version 2.15.1},
+ url = {https://CRAN.R-project.org/package=LearnBayes},
+}
+
+@Article{coda,
+ author = {Martyn Plummer and Nicky Best and Kate Cowles and Karen Vines},
+ title = {CODA: Convergence Diagnosis and Output Analysis for MCMC},
+ journal = {R News},
+ year = {2006},
+ volume = {6},
+ number = {1},
+ pages = {7--11},
+ file = {Rnews_2006-1.pdf:https\://www.r-project.org/doc/Rnews/Rnews_2006-1.pdf:PDF},
+ url = {https://journal.r-project.org/archive/},
+}
+
+@Manual{expm,
+ title = {expm: Matrix Exponential, Log, 'etc'},
+ author = {Vincent Goulet and Christophe Dutang and Martin Maechler and David Firth and Marina Shapira and Michael Stadelmann},
+ year = {2019},
+ note = {R package version 0.999-4},
+ url = {https://CRAN.R-project.org/package=expm},
+}
+
+@Manual{gmodels,
+ title = {gmodels: Various R Programming Tools for Model Fitting},
+ author = {Gregory R. Warnes and Ben Bolker and Thomas Lumley and Randall C Johnson. Contributions from Randall C. Johnson are Copyright SAIC-Frederick and Inc. Funded by the Intramural Research Program and of the NIH and National Cancer Institute and Center for Cancer Research under NCI Contract NO1-CO-12400.},
+ year = {2018},
+ note = {R package version 2.18.1},
+ url = {https://CRAN.R-project.org/package=gmodels},
+}
+
+@Manual{splines,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{knitr1,
+ title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+ author = {Yihui Xie},
+ year = {2019},
+ note = {R package version 1.25},
+ url = {https://yihui.name/knitr/},
+}
+
+@Book{knitr2,
+ title = {Dynamic Documents with {R} and knitr},
+ author = {Yihui Xie},
+ publisher = {Chapman and Hall/CRC},
+ address = {Boca Raton, Florida},
+ year = {2015},
+ edition = {2nd},
+ note = {ISBN 978-1498716963},
+ url = {https://yihui.name/knitr/},
+}
+
+@InCollection{knitr3,
+ booktitle = {Implementing Reproducible Computational Research},
+ editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
+ title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
+ author = {Yihui Xie},
+ publisher = {Chapman and Hall/CRC},
+ year = {2014},
+ note = {ISBN 978-1466561595},
+ url = {http://www.crcpress.com/product/isbn/9781466561595},
+}
+
+@Manual{shiny,
+ title = {shiny: Web Application Framework for R},
+ author = {Winston Chang and Joe Cheng and JJ Allaire and Yihui Xie and Jonathan McPherson},
+ year = {2019},
+ note = {R package version 1.4.0},
+ url = {https://CRAN.R-project.org/package=shiny},
+}
+
+@Manual{crosstalk,
+ title = {crosstalk: Inter-Widget Interactivity for HTML Widgets},
+ author = {Joe Cheng},
+ year = {2016},
+ note = {R package version 1.0.0},
+ url = {https://CRAN.R-project.org/package=crosstalk},
+}
+
+@Manual{manipulateWidget,
+ title = {manipulateWidget: Add Even More Interactivity to Interactive Charts},
+ author = {Jalal-Edine ZAWAM and Francois Guillem},
+ year = {2018},
+ note = {R package version 0.10.0},
+ url = {https://CRAN.R-project.org/package=manipulateWidget},
+}
+
+@Manual{loon,
+ title = {loon: Interactive Statistical Data Visualization},
+ author = {Adrian Waddell and R. Wayne Oldford},
+ year = {2019},
+ note = {R package version 1.2.3},
+ url = {https://CRAN.R-project.org/package=loon},
+}
+
+@Manual{base,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{rcdklibs,
+ title = {rcdklibs: The CDK Libraries Packaged for R},
+ author = {Rajarshi Guha},
+ year = {2017},
+ note = {R package version 2.0},
+ url = {https://CRAN.R-project.org/package=rcdklibs},
+}
+
+@Manual{fingerprint,
+ title = {fingerprint: Functions to Operate on Binary Fingerprint Data},
+ author = {Rajarshi Guha},
+ year = {2018},
+ note = {R package version 3.5.7},
+ url = {https://CRAN.R-project.org/package=fingerprint},
+}
+
+@Manual{rJava,
+ title = {rJava: Low-Level R to Java Interface},
+ author = {Simon Urbanek},
+ year = {2019},
+ note = {R package version 0.9-11},
+ url = {https://CRAN.R-project.org/package=rJava},
+}
+
+@Manual{itertools,
+ title = {itertools: Iterator Tools},
+ author = {Steve Weston and Hadley Wickham},
+ year = {2014},
+ note = {R package version 0.1-3},
+ url = {https://CRAN.R-project.org/package=itertools},
+}
+
+@Manual{RSQLite,
+ title = {RSQLite: 'SQLite' Interface for R},
+ author = {Kirill Muller and Hadley Wickham and David A. James and Seth Falcon},
+ year = {2019},
+ note = {R package version 2.1.2},
+ url = {https://CRAN.R-project.org/package=RSQLite},
+}
+
+@Manual{AnnotationDbi,
+ title = {AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor},
+ author = {Herv� Pag�s and Marc Carlson and Seth Falcon and Nianhua Li},
+ year = {2019},
+ note = {R package version 1.46.1},
+}
+
+@Manual{BiocFileCache,
+ title = {BiocFileCache: Manage Files Across Sessions},
+ author = {Lori Shepherd and Martin Morgan},
+ year = {2019},
+ note = {R package version 1.8.0},
+}
+
+@Manual{rappdirs,
+ title = {rappdirs: Application Directories: Determine Where to Save Data, Caches,
+and Logs},
+ author = {Sridhar Ratnakumar and Trent Mick and Trevor Davis},
+ year = {2016},
+ note = {R package version 0.3.1},
+ url = {https://CRAN.R-project.org/package=rappdirs},
+}
+
+@Manual{methods,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{pls,
+ title = {pls: Partial Least Squares and Principal Component Regression},
+ author = {Bj�rn-Helge Mevik and Ron Wehrens and Kristian Hovde Liland},
+ year = {2019},
+ note = {R package version 2.7-2},
+ url = {https://CRAN.R-project.org/package=pls},
+}
+
+@Manual{data.table,
+ title = {data.table: Extension of `data.frame`},
+ author = {Matt Dowle and Arun Srinivasan},
+ year = {2019},
+ note = {R package version 1.12.4},
+ url = {https://CRAN.R-project.org/package=data.table},
+}
+
+@Manual{pryr,
+ title = {pryr: Tools for Computing on the Language},
+ author = {Hadley Wickham},
+ year = {2018},
+ note = {R package version 0.1.4},
+ url = {https://CRAN.R-project.org/package=pryr},
+}
+
+@Manual{colortools,
+ title = {colortools: Tools for colors in a Hue-Saturation-Value (HSV) color model},
+ author = {Gaston Sanchez},
+ year = {2013},
+ note = {R package version 0.1.5},
+ url = {https://CRAN.R-project.org/package=colortools},
+}
+
+@Article{CAMERA,
+ author = {C. Kuhl and R. Tautenhahn and C. Boettcher and T. R. Larson and S. Neumann},
+ title = {CAMERA: an integrated strategy for compound spectra extraction
+ and annotation of liquid chromatography/mass spectrometry data sets},
+ journal = {Analytical Chemistry},
+ year = {2012},
+ volume = {84},
+ pages = {283--289},
+ url = {http://pubs.acs.org/doi/abs/10.1021/ac202450g},
+}
+
+@Manual{pacman,
+ title = {{pacman}: {P}ackage Management for {R}},
+ author = {Tyler W. Rinker and Dason Kurkiewicz},
+ address = {Buffalo, New York},
+ note = {version 0.5.0},
+ year = {2018},
+ url = {http://github.com/trinker/pacman},
+}
+
+@Manual{purrr,
+ title = {purrr: Functional Programming Tools},
+ author = {Lionel Henry and Hadley Wickham},
+ year = {2019},
+ note = {R package version 0.3.2},
+ url = {https://CRAN.R-project.org/package=purrr},
+}
+
+@Manual{RColorBrewer,
+ title = {RColorBrewer: ColorBrewer Palettes},
+ author = {Erich Neuwirth},
+ year = {2014},
+ note = {R package version 1.1-2},
+ url = {https://CRAN.R-project.org/package=RColorBrewer},
+}
+
+@Manual{magick,
+ title = {magick: Advanced Graphics and Image-Processing in R},
+ author = {Jeroen Ooms},
+ year = {2019},
+ note = {R package version 2.2},
+ url = {https://CRAN.R-project.org/package=magick},
+}
+
+@Book{ggplot2,
+ author = {Hadley Wickham},
+ title = {ggplot2: Elegant Graphics for Data Analysis},
+ publisher = {Springer-Verlag New York},
+ year = {2016},
+ isbn = {978-3-319-24277-4},
+ url = {https://ggplot2.tidyverse.org},
+}
+
+@Manual{reticulate,
+ title = {reticulate: Interface to 'Python'},
+ author = {Kevin Ushey and JJ Allaire and Yuan Tang},
+ year = {2019},
+ note = {R package version 1.13},
+ url = {https://CRAN.R-project.org/package=reticulate},
+}
+
+@Manual{dplyr,
+ title = {dplyr: A Grammar of Data Manipulation},
+ author = {Hadley Wickham and Romain Fran�ois and Lionel Henry and Kirill Muller},
+ year = {2019},
+ note = {R package version 0.8.3},
+ url = {https://CRAN.R-project.org/package=dplyr},
+}
+
+@Manual{stringr,
+ title = {stringr: Simple, Consistent Wrappers for Common String Operations},
+ author = {Hadley Wickham},
+ year = {2019},
+ note = {R package version 1.4.0},
+ url = {https://CRAN.R-project.org/package=stringr},
+}
+
+@Manual{doParallel,
+ title = {doParallel: Foreach Parallel Adaptor for the 'parallel' Package},
+ author = {Microsoft Corporation and Steve Weston},
+ year = {2019},
+ note = {R package version 1.0.15},
+ url = {https://CRAN.R-project.org/package=doParallel},
+}
+
+@Manual{iterators,
+ title = {iterators: Provides Iterator Construct},
+ author = {Revolution Analytics and Steve Weston},
+ year = {2019},
+ note = {R package version 1.0.12},
+ url = {https://CRAN.R-project.org/package=iterators},
+}
+
+@Manual{foreach,
+ title = {foreach: Provides Foreach Looping Construct},
+ author = {{Microsoft} and Steve Weston},
+ year = {2019},
+ note = {R package version 1.4.7},
+ url = {https://CRAN.R-project.org/package=foreach},
+}
+
+@Manual{protViz,
+ title = {protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics},
+ author = {Christian Panse and Jonas Grossmann},
+ year = {2019},
+ note = {R package version 0.4.0; https://CRAN.R-project.org/package=protViz},
+}
+
+@Manual{cleaver,
+ title = {cleaver: Cleavage of Polypeptide Sequences},
+ author = {Sebastian Gibb},
+ year = {2019},
+ note = {R package version 1.22.0},
+ url = {https://github.com/sgibb/cleaver/},
+}
+
+@Article{MALDIquant,
+ title = {{MALDI}quant: a versatile {R} package for the analysis of mass spectrometry data},
+ author = {Sebastian Gibb and Korbinian Strimmer},
+ volume = {28},
+ number = {17},
+ pages = {2270--2271},
+ year = {2012},
+ doi = {10.1093/bioinformatics/bts447},
+ url = {http://bioinformatics.oxfordjournals.org/content/28/17/2270.abstract},
+ eprint = {http://bioinformatics.oxfordjournals.org/content/28/17/2270.full.pdf+html},
+ journal = {Bioinformatics},
+ publisher = {Oxford University Press},
+}
+
+@Manual{Biostrings,
+ title = {Biostrings: Efficient manipulation of biological strings},
+ author = {H. Pag�s and P. Aboyoun and R. Gentleman and S. DebRoy},
+ year = {2019},
+ note = {R package version 2.52.0},
+}
+
+@Manual{XVector,
+ title = {XVector: Foundation of external vector representation and manipulation in
+Bioconductor},
+ author = {Herv� Pag�s and Patrick Aboyoun},
+ year = {2019},
+ note = {R package version 0.24.0},
+}
+
+@Article{IRanges,
+ title = {Software for Computing and Annotating Genomic Ranges},
+ author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin Morgan and Vincent Carey},
+ year = {2013},
+ journal = {{PLoS} Computational Biology},
+ volume = {9},
+ issue = {8},
+ doi = {10.1371/journal.pcbi.1003118},
+ url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
+}
+
+@Article{Cardinal,
+ title = {Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments},
+ author = {Kyle D. Bemis and April Harry and Livia S. Eberlin and Christina Ferreira and Stephanie M. {van de Ven} and Parag Mallick and Mark Stolowitz and Olga Vitek},
+ journal = {Bioinformatics},
+ year = {2015},
+ doi = {10.1093/bioinformatics/btv146},
+}
+
+@Manual{ProtGenerics,
+ title = {ProtGenerics: S4 generic functions for Bioconductor proteomics infrastructure},
+ author = {Laurent Gatto},
+ year = {2019},
+ note = {R package version 1.16.0},
+ url = {https://github.com/lgatto/ProtGenerics},
+}
+
+@Manual{S4Vectors,
+ title = {S4Vectors: Foundation of vector-like and list-like containers in
+Bioconductor},
+ author = {H. Pag�s and M. Lawrence and P. Aboyoun},
+ year = {2019},
+ note = {R package version 0.22.1},
+}
+
+@Manual{tcltk,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{stats4,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Article{EBImage,
+ title = {EBImage---an R package for image processing with applications to cellular phenotypes},
+ author = {Gregoire Pau and Florian Fuchs and Oleg Sklyar and Michael Boutros and Wolfgang Huber},
+ journal = {Bioinformatics},
+ volume = {26},
+ number = {7},
+ pages = {979--981},
+ year = {2010},
+ doi = {10.1093/bioinformatics/btq046},
+}
+
+@Manual{BiocParallel,
+ title = {BiocParallel: Bioconductor facilities for parallel evaluation},
+ author = {Martin Morgan and Valerie Obenchain and Michel Lang and Ryan Thompson and Nitesh Turaga},
+ year = {2019},
+ note = {R package version 1.18.1},
+ url = {https://github.com/Bioconductor/BiocParallel},
+}
+
+@Article{BiocGenerics,
+ author = {{Huber} and {W.} and {Carey} and V. J. and {Gentleman} and {R.} and {Anders} and {S.} and {Carlson} and {M.} and {Carvalho} and B. S. and {Bravo} and H. C. and {Davis} and {S.} and {Gatto} and {L.} and {Girke} and {T.} and {Gottardo} and {R.} and {Hahne} and {F.} and {Hansen} and K. D. and {Irizarry} and R. A. and {Lawrence} and {M.} and {Love} and M. I. and {MacDonald} and {J.} and {Obenchain} and {V.} and {{Ole's}} and A. K. and {{Pag`es}} and {H.} and {Reyes} and {A.} and {Shannon} and {P.} and {Smyth} and G. K. and {Tenenbaum} and {D.} and {Waldron} and {L.} and {Morgan} and {M.}},
+ title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
+ journal = {Nature Methods},
+ year = {2015},
+ volume = {12},
+ number = {2},
+ pages = {115--121},
+ url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
+}
+
+@Manual{parallel,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{stats,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{graphics,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{grDevices,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{utils,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{datasets,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Article{Rdisop1,
+ author = {Sebastian B"ocker and Matthias Letzel and Zsuzsanna Lipt{'a}k and Anton Pervukhin},
+ title = {{SIRIUS}: Decomposing isotope patterns for metabolite identification},
+ journal = {Bioinformatics},
+ year = {2009},
+ volume = {25},
+ number = {2},
+ pages = {218--224},
+ doi = {10.1093/bioinformatics/btn603},
+ pmid = {19015140},
+}
+
+@Article{Rdisop2,
+ author = {Sebastian B"ocker and Zsuzsanna Lipt'ak and Marcel Martin and Anton Pervukhin and Henner Sudek},
+ title = {{DECOMP}---from interpreting Mass Spectrometry peaks to solving the {Money} {Changing} {Problem}},
+ journal = {Bioinformatics},
+ year = {2008},
+ volume = {24},
+ number = {4},
+ pages = {591--593},
+ doi = {10.1093/bioinformatics/btm631},
+ pmid = {18174179},
+}
+
+@InProceedings{Rdisop3,
+ author = {Sebastian B"ocker and Matthias Letzel and Zsuzsanna Lipt{'a}k and Anton Pervukhin},
+ title = {Decomposing metabolomic isotope patterns},
+ booktitle = {Proc. of Workshop on Algorithms in Bioinformatics (WABI 2006)},
+ publisher = {Springer, Berlin},
+ year = {2006},
+ volume = {4175},
+ pages = {12--23},
+ series = {Lect. Notes Comput. Sci.},
+}
+
+@Article{Rdisop4,
+ author = {Sebastian B"ocker and Zsuzsanna Lipt{'a}k},
+ title = {A fast and simple algorithm for the Money Changing Problem.},
+ journal = {Algorithmica},
+ year = {2007},
+ volume = {48},
+ number = {4},
+ pages = {413-432},
+ doi = {10.1007/s00453-007-0162-8},
+}
+
+@Article{Rcpp1,
+ title = {{Rcpp}: Seamless {R} and {C++} Integration},
+ author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
+ journal = {Journal of Statistical Software},
+ year = {2011},
+ volume = {40},
+ number = {8},
+ pages = {1--18},
+ url = {http://www.jstatsoft.org/v40/i08/},
+ doi = {10.18637/jss.v040.i08},
+}
+
+@Book{Rcpp2,
+ title = {Seamless {R} and {C++} Integration with {Rcpp}},
+ author = {Dirk Eddelbuettel},
+ publisher = {Springer},
+ address = {New York},
+ year = {2013},
+ note = {ISBN 978-1-4614-6867-7},
+ doi = {10.1007/978-1-4614-6868-4},
+}
+
+@Article{Rcpp3,
+ title = {{Extending extit{R} with extit{C++}: A Brief Introduction to extit{Rcpp}}},
+ author = {Dirk Eddelbuettel and James Joseph Balamuta},
+ journal = {PeerJ Preprints},
+ year = {2017},
+ month = {aug},
+ volume = {5},
+ pages = {e3188v1},
+ issn = {2167-9843},
+ url = {https://doi.org/10.7287/peerj.preprints.3188v1},
+ doi = {10.7287/peerj.preprints.3188v1},
+}
+
+@Manual{devtools,
+ title = {devtools: Tools to Make Developing R Packages Easier},
+ author = {Hadley Wickham and Jim Hester and Winston Chang},
+ year = {2019},
+ note = {R package version 2.2.1},
+ url = {https://CRAN.R-project.org/package=devtools},
+}
+
+@Manual{fs,
+ title = {fs: Cross-Platform File System Operations Based on 'libuv'},
+ author = {Jim Hester and Hadley Wickham},
+ year = {2019},
+ note = {R package version 1.3.1},
+ url = {https://CRAN.R-project.org/package=fs},
+}
+
+@Manual{processx,
+ title = {processx: Execute and Control System Processes},
+ author = {Gabor Csardi and Winston Chang},
+ year = {2019},
+ note = {R package version 3.4.1},
+ url = {https://CRAN.R-project.org/package=processx},
+}
+
+@Article{spdep1,
+ author = {Roger Bivand and David W. S. Wong},
+ title = {Comparing implementations of global and local indicators of spatial association},
+ journal = {TEST},
+ year = {2018},
+ volume = {27},
+ number = {3},
+ pages = {716--748},
+ url = {https://doi.org/10.1007/s11749-018-0599-x},
+}
+
+@Book{spdep2,
+ author = {Roger S. Bivand and Edzer Pebesma and Virgilio Gomez-Rubio},
+ title = {Applied spatial data analysis with {R}, Second edition},
+ year = {2013},
+ publisher = {Springer, NY},
+ url = {http://www.asdar-book.org/},
+}
+
+@Article{zoo,
+ title = {zoo: S3 Infrastructure for Regular and Irregular Time Series},
+ author = {Achim Zeileis and Gabor Grothendieck},
+ journal = {Journal of Statistical Software},
+ year = {2005},
+ volume = {14},
+ number = {6},
+ pages = {1--27},
+ doi = {10.18637/jss.v014.i06},
+}
+
+@Manual{FTICRMS,
+ title = {FTICRMS: Programs for Analyzing Fourier Transform-Ion Cyclotron Resonance
+Mass Spectrometry Data},
+ author = {Don Barkauskas},
+ year = {2012},
+ note = {R package version 0.8},
+ url = {https://CRAN.R-project.org/package=FTICRMS},
+}
+
+@Manual{KEGGREST,
+ title = {KEGGREST: Client-side REST access to KEGG},
+ author = {Dan Tenenbaum},
+ year = {2019},
+ note = {R package version 1.24.1},
+}
+
+@Manual{OrgMassSpecR,
+ title = {OrgMassSpecR: Organic Mass Spectrometry},
+ author = {Nathan Dodder},
+ year = {2017},
+ note = {R package version 0.5-3},
+ url = {https://CRAN.R-project.org/package=OrgMassSpecR},
+}
+
+@Article{enviPat,
+ title = {Accelerated Isotope Fine Structure Calculation Using Pruned Transition Trees},
+ author = {Martin Loos and Christian Gerber and Francesco Corona and Juliane Hollender and Heinz Singer},
+ journal = {Analytical Chemistry},
+ volume = {87},
+ number = {11},
+ pages = {5738-5744},
+ year = {2015},
+ url = {http://pubs.acs.org/doi/abs/10.1021/acs.analchem.5b00941},
+}
+
+@Manual{rgl,
+ title = {rgl: 3D Visualization Using OpenGL},
+ author = {Daniel Adler and Duncan Murdoch and others},
+ year = {2019},
+ note = {R package version 0.100.30},
+ url = {https://CRAN.R-project.org/package=rgl},
+}
+
+@Manual{tkrplot,
+ title = {tkrplot: TK Rplot},
+ author = {Luke Tierney},
+ year = {2018},
+ note = {R package version 0.0-24},
+ url = {https://CRAN.R-project.org/package=tkrplot},
+}
+
+@Book{multtest,
+ title = {Multiple Testing Procedures: R multtest Package and Applications to Genomics, in Bioinformatics and Computational Biology Solutions Using R and Bioconductor},
+ year = {2005},
+ author = {Katherine S. Pollard and Sandrine Dudoit and Mark J. {van der Laan}},
+ publisher = {Springer},
+}
+
+@Manual{XML,
+ title = {XML: Tools for Parsing and Generating XML Within R and S-Plus},
+ author = {Duncan Temple Lang and the CRAN Team},
+ year = {2019},
+ note = {R package version 3.98-1.20},
+ url = {https://CRAN.R-project.org/package=XML},
+}
+
+@Manual{BiocManager,
+ title = {BiocManager: Access the Bioconductor Project Package Repository},
+ author = {Martin Morgan},
+ year = {2019},
+ note = {R package version 1.30.9},
+ url = {https://CRAN.R-project.org/package=BiocManager},
+}
+
+@Article{randomForest,
+ title = {Classification and Regression by randomForest},
+ author = {Andy Liaw and Matthew Wiener},
+ journal = {R News},
+ year = {2002},
+ volume = {2},
+ number = {3},
+ pages = {18-22},
+ url = {https://CRAN.R-project.org/doc/Rnews/},
+}
+
+@Manual{rfviz,
+ title = {rfviz: Interactive Visualization Tool for Random Forests},
+ author = {Chris Beckett},
+ year = {2018},
+ note = {R package version 1.0.0},
+ url = {https://CRAN.R-project.org/package=rfviz},
+}
+
+@Article{rcdk,
+ author = {Rajarshi Guha},
+ journal = {Journal of Statistical Software},
+ number = {6},
+ title = {Chemical Informatics Functionality in R},
+ volume = {18},
+ year = {2007},
+}
+
+@Article{igraph,
+ title = {The igraph software package for complex network research},
+ author = {Gabor Csardi and Tamas Nepusz},
+ journal = {InterJournal},
+ volume = {Complex Systems},
+ pages = {1695},
+ year = {2006},
+ url = {http://igraph.org},
+}
+
+@TechReport{colorspace1,
+ title = {{colorspace}: A Toolbox for Manipulating and Assessing Colors and Palettes},
+ author = {Achim Zeileis and Jason C. Fisher and Kurt Hornik and Ross Ihaka and Claire D. McWhite and Paul Murrell and Reto Stauffer and Claus O. Wilke},
+ year = {2019},
+ institution = {arXiv.org E-Print Archive},
+ type = {arXiv},
+ number = {1903.06490},
+ month = {March},
+ url = {http://arxiv.org/abs/1903.06490},
+}
+
+@Article{colorspace2,
+ title = {Escaping {RGB}land: Selecting Colors for Statistical Graphics},
+ author = {Achim Zeileis and Kurt Hornik and Paul Murrell},
+ journal = {Computational Statistics \& Data Analysis},
+ year = {2009},
+ volume = {53},
+ number = {9},
+ pages = {3259--3270},
+ doi = {10.1016/j.csda.2008.11.033},
+}
+
+@Article{colorspace3,
+ title = {Somewhere over the Rainbow: How to Make Effective Use of Colors in Meteorological Visualizations},
+ author = {Reto Stauffer and Georg J. Mayr and Markus Dabernig and Achim Zeileis},
+ journal = {Bulletin of the American Meteorological Society},
+ year = {2009},
+ volume = {96},
+ number = {2},
+ pages = {203--216},
+ doi = {10.1175/BAMS-D-13-00155.1},
+}
+
+@Manual{UniProt.ws,
+ title = {UniProt.ws: R Interface to UniProt Web Services},
+ author = {Marc Carlson},
+ year = {2019},
+ note = {R package version 2.24.2},
+}
+
+@Manual{gridExtra,
+ title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
+ author = {Baptiste Auguie},
+ year = {2017},
+ note = {R package version 2.3},
+ url = {https://CRAN.R-project.org/package=gridExtra},
+}
+
+@Manual{grid,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2019},
+ url = {https://www.R-project.org/},
+}
+
+@Manual{gtable,
+ title = {gtable: Arrange 'Grobs' in Tables},
+ author = {Hadley Wickham and Thomas Lin Pedersen},
+ year = {2019},
+ note = {R package version 0.3.0},
+ url = {https://CRAN.R-project.org/package=gtable},
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}