diff --git a/404.html b/404.html index 4300708..1c1cea9 100644 --- a/404.html +++ b/404.html @@ -40,7 +40,7 @@ DeconvoBuddies - 0.99.1 + 0.99.2 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 51ec487..149b833 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ DeconvoBuddies - 0.99.1 + 0.99.2 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 5083d9e..6309694 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ DeconvoBuddies - 0.99.1 + 0.99.2 diff --git a/SUPPORT.html b/SUPPORT.html index 2bfe5f1..2276606 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ DeconvoBuddies - 0.99.1 + 0.99.2 diff --git a/articles/DeconvoBuddies.html b/articles/DeconvoBuddies.html index e7e7b58..b52c044 100644 --- a/articles/DeconvoBuddies.html +++ b/articles/DeconvoBuddies.html @@ -39,7 +39,7 @@ DeconvoBuddies - 0.99.1 + 0.99.2 @@ -174,7 +174,7 @@

Citing DeconvoBuddies#> doi:10.18129/B9.bioc.DeconvoBuddies #> <https://doi.org/10.18129/B9.bioc.DeconvoBuddies>, #> https://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R -#> package version 0.99.1, +#> package version 0.99.2, #> <http://www.bioconductor.org/packages/DeconvoBuddies>. #> #> Huuki-Myers LA, Montgomery KD, Kwon SH, Cinquemani S, Eagles NJ, @@ -221,7 +221,7 @@

Access Data
 ## Access and snRNA-seq example data
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:11:16.065139 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-10-18 15:53:28.706453 loading file /github/home/.cache/R/BiocFileCache/259727d5821_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 
 ## Explore snRNA-seq data in sce_DLPFC_example
 sce_DLPFC_example
@@ -240,7 +240,7 @@ 
Access Data## Access Bulk RNA-seq data
 if (!exists("rse_gene")) rse_gene <- fetch_deconvo_data("rse_gene")
-#> 2024-10-18 15:11:17.691504 loading file /github/home/.cache/R/BiocFileCache/39c65f2ee1_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
+#> 2024-10-18 15:53:30.883069 loading file /github/home/.cache/R/BiocFileCache/25978734f9f_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
 
 ## Explore bulk data in rse_gene
 rse_gene
@@ -504,9 +504,9 @@ 
Reproducibilitylibrary("knitr")
 knit("DeconvoBuddies.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-10-18 15:11:22 UTC"
+
#> [1] "2024-10-18 15:53:35 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 18.251 secs
+
#> Time difference of 20.141 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -563,7 +563,7 @@ 
Reproducibility#>  data.table             1.16.2    2024-10-10 [1] RSPM (R 4.4.0)
 #>  DBI                    1.2.3     2024-06-02 [1] RSPM (R 4.4.0)
 #>  dbplyr                 2.5.0     2024-03-19 [1] RSPM (R 4.4.0)
-#>  DeconvoBuddies       * 0.99.1    2024-10-18 [1] Bioconductor
+#>  DeconvoBuddies       * 0.99.2    2024-10-18 [1] Bioconductor
 #>  DelayedArray           0.31.14   2024-10-03 [1] Bioconductor 3.20 (R 4.4.1)
 #>  desc                   1.4.3     2023-12-10 [2] RSPM (R 4.4.0)
 #>  digest                 0.6.37    2024-08-19 [2] RSPM (R 4.4.0)
@@ -719,7 +719,7 @@ 
Bibliographyhttps://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies
-- R package version 0.99.1. 2024. DOI:
+- R package version 0.99.2. 2024. DOI:
 10.18129/B9.bioc.DeconvoBuddies.
 URL:
 http://www.bioconductor.org/packages/DeconvoBuddies.
diff --git a/articles/Deconvolution_Benchmark_DLPFC.html b/articles/Deconvolution_Benchmark_DLPFC.html
index 581613d..2924720 100644
--- a/articles/Deconvolution_Benchmark_DLPFC.html
+++ b/articles/Deconvolution_Benchmark_DLPFC.html
@@ -39,7 +39,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
@@ -283,7 +283,7 @@ 
Bulk RNA-seq data
 ## use fetch deconvo data to load rse_gene
 rse_gene <- fetch_deconvo_data("rse_gene")
-#> 2024-10-18 15:11:38.148787 loading file /github/home/.cache/R/BiocFileCache/39c65f2ee1_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
+#> 2024-10-18 15:53:52.827281 loading file /github/home/.cache/R/BiocFileCache/25978734f9f_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
 rse_gene
 #> class: RangedSummarizedExperiment 
 #> dim: 21745 110 
@@ -319,7 +319,7 @@ 
Reference snRNA-seq data
 ## Use spatialLIBD to fetch the snRNA-seq dataset used in this project
 sce_path_zip <- fetch_deconvo_data("sce")
-#> 2024-10-18 15:11:39.59906 loading file /github/home/.cache/R/BiocFileCache/39c46de306b_sce_DLPFC_annotated.zip%3Fdl%3D1
+#> 2024-10-18 15:53:55.287473 loading file /github/home/.cache/R/BiocFileCache/25949214610_sce_DLPFC_annotated.zip%3Fdl%3D1
 
 ## unzip and load the data
 sce_path <- unzip(sce_path_zip, exdir = tempdir())
@@ -877,9 +877,9 @@ 
Reproducibilitylibrary("knitr")
 knit("Deconvolution_Benchmark_DLPFC.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-10-18 15:12:39 UTC"

+
#> [1] "2024-10-18 15:54:56 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 1.216 mins

+
#> Time difference of 1.279 mins

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -937,7 +937,7 @@ 
Reproducibility#>  data.table             1.16.2    2024-10-10 [1] RSPM (R 4.4.0)
 #>  DBI                    1.2.3     2024-06-02 [1] RSPM (R 4.4.0)
 #>  dbplyr                 2.5.0     2024-03-19 [1] RSPM (R 4.4.0)
-#>  DeconvoBuddies       * 0.99.1    2024-10-18 [1] Bioconductor
+#>  DeconvoBuddies       * 0.99.2    2024-10-18 [1] Bioconductor
 #>  DelayedArray           0.31.14   2024-10-03 [1] Bioconductor 3.20 (R 4.4.1)
 #>  desc                   1.4.3     2023-12-10 [2] RSPM (R 4.4.0)
 #>  digest                 0.6.37    2024-08-19 [2] RSPM (R 4.4.0)
@@ -1101,7 +1101,7 @@ 
Bibliographyhttps://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies
-- R package version 0.99.1. 2024. DOI:
+- R package version 0.99.2. 2024. DOI:
 10.18129/B9.bioc.DeconvoBuddies.
 URL:
 http://www.bioconductor.org/packages/DeconvoBuddies.
diff --git a/articles/Marker_Finding.html b/articles/Marker_Finding.html
index fd2628b..6d80ee2 100644
--- a/articles/Marker_Finding.html
+++ b/articles/Marker_Finding.html
@@ -39,7 +39,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
@@ -254,7 +254,7 @@ 
2. Download DLPFC snRNA-seq data.
 ## Use spatialLIBD to fetch the snRNA-seq dataset
 sce_path_zip <- fetch_deconvo_data("sce")
-#> 2024-10-18 15:12:57.078814 loading file /github/home/.cache/R/BiocFileCache/39c46de306b_sce_DLPFC_annotated.zip%3Fdl%3D1
+#> 2024-10-18 15:55:16.912696 loading file /github/home/.cache/R/BiocFileCache/25949214610_sce_DLPFC_annotated.zip%3Fdl%3D1
 
 ## unzip and load the data
 sce_path <- unzip(sce_path_zip, exdir = tempdir())
@@ -684,9 +684,9 @@ 
Reproducibilitylibrary("knitr")
 knit("Marker_Finding.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-10-18 15:15:11 UTC"

+
#> [1] "2024-10-18 15:57:31 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 2.439 mins

+
#> Time difference of 2.477 mins

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -743,7 +743,7 @@ 
Reproducibility#>  data.table             1.16.2    2024-10-10 [1] RSPM (R 4.4.0)
 #>  DBI                    1.2.3     2024-06-02 [1] RSPM (R 4.4.0)
 #>  dbplyr                 2.5.0     2024-03-19 [1] RSPM (R 4.4.0)
-#>  DeconvoBuddies       * 0.99.1    2024-10-18 [1] Bioconductor
+#>  DeconvoBuddies       * 0.99.2    2024-10-18 [1] Bioconductor
 #>  DelayedArray           0.31.14   2024-10-03 [1] Bioconductor 3.20 (R 4.4.1)
 #>  desc                   1.4.3     2023-12-10 [2] RSPM (R 4.4.0)
 #>  digest                 0.6.37    2024-08-19 [2] RSPM (R 4.4.0)
@@ -903,7 +903,7 @@ 
Bibliographyhttps://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies
-- R package version 0.99.1. 2024. DOI:
+- R package version 0.99.2. 2024. DOI:
 10.18129/B9.bioc.DeconvoBuddies.
 URL:
 http://www.bioconductor.org/packages/DeconvoBuddies.
diff --git a/articles/index.html b/articles/index.html
index 625e6d5..442e87c 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
diff --git a/authors.html b/authors.html
index da81e3e..89b29b8 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
@@ -83,14 +83,14 @@ 
Citation

 
     
Huuki-Myers LA, Maynard KR, Hicks SC, Zandi P, Kleinman JE, Hyde TM, Goes FS, Collado-Torres L (2024).
 DeconvoBuddies: a R/Bioconductor package with deconvolution helper functions.
-doi:10.18129/B9.bioc.DeconvoBuddies, https://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R package version 0.99.1, http://www.bioconductor.org/packages/DeconvoBuddies.
+doi:10.18129/B9.bioc.DeconvoBuddies, https://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R package version 0.99.2, http://www.bioconductor.org/packages/DeconvoBuddies.
 

     
@Manual{,
   title = {DeconvoBuddies: a R/Bioconductor package with deconvolution helper functions},
   author = {Louise A. Huuki-Myers and Kristen R. Maynard and Stephanie C. Hicks and Peter Zandi and Joel E. Kleinman and Tom M. Hyde and Fernando S. Goes and Leonardo Collado-Torres},
   year = {2024},
   url = {http://www.bioconductor.org/packages/DeconvoBuddies},
-  note = {https://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R package version 0.99.1},
+  note = {https://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R package version 0.99.2},
   doi = {10.18129/B9.bioc.DeconvoBuddies},
 }

     
Huuki-Myers LA, Montgomery KD, Kwon SH, Cinquemani S, Eagles NJ, Gonzalez-Padilla D, Maden SK, Kleinman JE, Hyde TM, Hicks SC, Maynard KR, Collado-Torres L (2024).
diff --git a/index.html b/index.html
index 5fd91b9..2f5caf2 100644
--- a/index.html
+++ b/index.html
@@ -41,7 +41,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
diff --git a/news/index.html b/news/index.html
index 9556bfe..7049b8d 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
diff --git a/pkgdown.yml b/pkgdown.yml
index caeabeb..d480e20 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,4 +5,4 @@ articles:
   DeconvoBuddies: DeconvoBuddies.html
   Deconvolution_Benchmark_DLPFC: Deconvolution_Benchmark_DLPFC.html
   Marker_Finding: Marker_Finding.html
-last_built: 2024-10-18T15:10Z
+last_built: 2024-10-18T15:52Z
diff --git a/reference/RNAScope_prop.html b/reference/RNAScope_prop.html
index 2f5cbf9..2d7ee7f 100644
--- a/reference/RNAScope_prop.html
+++ b/reference/RNAScope_prop.html
@@ -19,7 +19,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
diff --git a/reference/create_cell_colors.html b/reference/create_cell_colors.html
index ddb7bcc..2cc7e40 100644
--- a/reference/create_cell_colors.html
+++ b/reference/create_cell_colors.html
@@ -19,7 +19,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
diff --git a/reference/dot-get_mean_ratio2.html b/reference/dot-get_mean_ratio2.html
index f8974ce..e102205 100644
--- a/reference/dot-get_mean_ratio2.html
+++ b/reference/dot-get_mean_ratio2.html
@@ -18,7 +18,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
@@ -117,7 +117,7 @@ 
Details

     
Examples

     
#' ## load example SingleCellExperiment
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:10:23.238305 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-10-18 15:52:27.369629 loading file /github/home/.cache/R/BiocFileCache/259727d5821_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 
 ## Get the mean ratio for each gene for each cell type defined in `cellType_broad_hc`
 .get_mean_ratio2(sce_DLPFC_example, cellType_col = "cellType_broad_hc")
diff --git a/reference/est_prop.html b/reference/est_prop.html
index 7c49781..c698369 100644
--- a/reference/est_prop.html
+++ b/reference/est_prop.html
@@ -17,7 +17,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     

 
diff --git a/reference/fetch_deconvo_data.html b/reference/fetch_deconvo_data.html
index 5435c62..860187e 100644
--- a/reference/fetch_deconvo_data.html
+++ b/reference/fetch_deconvo_data.html
@@ -19,7 +19,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
@@ -138,7 +138,7 @@ 
Examples

 ## A RangedSummarizedExperiment (41.16 MB)
 
 if (!exists("rse-gene")) rse_gene <- fetch_deconvo_data("rse_gene")
-#> 2024-10-18 15:10:25.900874 loading file /github/home/.cache/R/BiocFileCache/39c65f2ee1_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
+#> 2024-10-18 15:52:30.989515 loading file /github/home/.cache/R/BiocFileCache/25978734f9f_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
 
 ## explore bulk data
 rse_gene
@@ -157,7 +157,7 @@ 
Examples

 ## load example snRNA-seq data
 ## A SingleCellExperiment (4.79 MB)
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:10:26.807087 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-10-18 15:52:32.40191 loading file /github/home/.cache/R/BiocFileCache/259727d5821_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 
 ## explore example sce data
 sce_DLPFC_example
diff --git a/reference/findMarkers_1vAll.html b/reference/findMarkers_1vAll.html
index 32378e7..bd18669 100644
--- a/reference/findMarkers_1vAll.html
+++ b/reference/findMarkers_1vAll.html
@@ -18,7 +18,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
@@ -152,7 +152,7 @@ 
Details

     
Examples

     
## load example SingleCellExperiment
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:10:29.25446 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-10-18 15:52:35.675148 loading file /github/home/.cache/R/BiocFileCache/259727d5821_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 ## Explore properties of the sce object
 sce_DLPFC_example
 #> class: SingleCellExperiment 
@@ -198,14 +198,14 @@ 
Examples

     mod = "~BrNum"
 )
 #> Running 1vALL Testing for up-regulated genes
-#> 2024-10-18 15:10:29.531185 - Find markers for: Oligo
-#> 2024-10-18 15:10:30.03004 - Find markers for: Excit
-#> 2024-10-18 15:10:30.310071 - Find markers for: Inhib
-#> 2024-10-18 15:10:31.355623 - Find markers for: Micro
-#> 2024-10-18 15:10:31.636121 - Find markers for: OPC
-#> 2024-10-18 15:10:31.915212 - Find markers for: EndoMural
-#> 2024-10-18 15:10:32.20635 - Find markers for: Astro
-#> 2024-10-18 15:10:32.525246 - Building Table
+#> 2024-10-18 15:52:35.968444 - Find markers for: Oligo
+#> 2024-10-18 15:52:36.452888 - Find markers for: Excit
+#> 2024-10-18 15:52:36.740822 - Find markers for: Inhib
+#> 2024-10-18 15:52:37.871584 - Find markers for: Micro
+#> 2024-10-18 15:52:38.21487 - Find markers for: OPC
+#> 2024-10-18 15:52:38.552915 - Find markers for: EndoMural
+#> 2024-10-18 15:52:38.894096 - Find markers for: Astro
+#> 2024-10-18 15:52:39.267719 - Building Table
 #> ** Done! **
 
 ## explore output, top markers have high logFC
diff --git a/reference/get_mean_ratio.html b/reference/get_mean_ratio.html
index 63744c9..2fdd834 100644
--- a/reference/get_mean_ratio.html
+++ b/reference/get_mean_ratio.html
@@ -18,7 +18,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     

 
@@ -139,7 +139,7 @@ 
Details

     
Examples

     
## load example SingleCellExperiment
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:10:33.630712 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-10-18 15:52:41.138164 loading file /github/home/.cache/R/BiocFileCache/259727d5821_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 ## Explore properties of the sce object
 sce_DLPFC_example
 #> class: SingleCellExperiment 
diff --git a/reference/index.html b/reference/index.html
index 1dc003a..2ffaf25 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     

 
diff --git a/reference/make_test_sce.html b/reference/make_test_sce.html
index 70c2737..39aabeb 100644
--- a/reference/make_test_sce.html
+++ b/reference/make_test_sce.html
@@ -18,7 +18,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
diff --git a/reference/marker_test.html b/reference/marker_test.html
index dd95deb..578c3b2 100644
--- a/reference/marker_test.html
+++ b/reference/marker_test.html
@@ -18,7 +18,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
diff --git a/reference/plot_composition_bar.html b/reference/plot_composition_bar.html
index 0a33b80..620dc15 100644
--- a/reference/plot_composition_bar.html
+++ b/reference/plot_composition_bar.html
@@ -19,7 +19,7 @@
       
       
         DeconvoBuddies
-        0.99.1
+        0.99.2
       
     
 
diff --git a/reference/plot_gene_express.html b/reference/plot_gene_express.html
index 5a74ddb..468957a 100644
--- a/reference/plot_gene_express.html
+++ b/reference/plot_gene_express.html
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Examples

 
 # Access example data
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:10:38.800735 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
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 ## plot expression of two genes
 plot_gene_express(sce = sce_DLPFC_example, category = "cellType_broad_hc", genes = c("GAD2", "CD22"))
diff --git a/reference/plot_marker_express.html b/reference/plot_marker_express.html
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Examples

     
## Download the processed study data from
 ## <https://github.com/LieberInstitute/Human_DLPFC_Deconvolution>.
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:10:42.575778 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
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 ## Plot the top markers for Astrocytes
 plot_marker_express(
diff --git a/reference/plot_marker_express_ALL.html b/reference/plot_marker_express_ALL.html
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See also

     
Examples

     
#' ## Fetch sce example data
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:10:45.378923 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
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 # Plot marker gene expression to PDF, one page per cell type in stats
 pdf_file <- tempfile("test_marker_expression_ALL", fileext = ".pdf")
diff --git a/reference/plot_marker_express_List.html b/reference/plot_marker_express_List.html
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See also

     
Examples

     
## Fetch sce example data
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-10-18 15:11:00.60897 loading file /github/home/.cache/R/BiocFileCache/39c5bf0d43_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-10-18 15:53:11.270238 loading file /github/home/.cache/R/BiocFileCache/259727d5821_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 
 ## Create list-of-lists of genes to plot, names of sub-list become title of page
 my_gene_list <- list(Inhib = c("GAD2", "SAMD5"), Astro = c("RGS20", "PRDM16"))
diff --git a/reference/rse_bulk_test.html b/reference/rse_bulk_test.html
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