version 0.1

DESCRIPTION

@@ -14,8 +14,11 @@ LazyLoad: yes
 Depends:
     R (>= 3.0.0)
 Imports:
+    AnnotationHub,
+    biomaRt,
     data.table,
     DBI,
+    hash,
     RMySQL,
     GenomicFeatures,
     GenomicRanges,

README.md

@@ -0,0 +1,48 @@
+# ciRcus: an R package for circRNA manipulation, annotation and analysis
+
+ciRcus is a collection of functions for everyday munging of circRNA data.
+In its current, preliminary version, it can take lists of putative splice junctions generated using find_circ.py ([Memczak et al. 2013](http://www.nature.com/nature/journal/v495/n7441/full/nature11928.html), [circBase](http://www.circbase.org)) as input, and perform following annotation steps:
+
+* quality filtering
+* suggesting a host gene candidate was spliced from
+* calculating circular-to-linear ratio
+* describe gene features circRNA candidate was spliced from
+* report if circRNA's spliced junctions are already annotated as linear exon-intron junctions
+* generate read count histogram and gene feature pie-charts
+
+# Installation
+
+### Install via install_github()
+```R
+#' Install dependecies
+install.packages( c("data.table", "DBI", "hash", "ggplot2", "RMySQL", "devtools"))
+source("http://bioconductor.org/biocLite.R")
+biocLite(c("GenomicRanges","GenomicFeatures", "IRanges", "biomaRt", "AnnotationHub"))
+
+#' install the package
+library(devtools)
+install_github("BIMSBbioinfo/ciRcus",build_vignettes=FALSE)
+
+
+```
+
+# Using the package
+### Build TxDb object with genomic features and save locally
+Load genomic features from Ensembl and build a database for later (re)use. Currently supported assemblies are hg19, hg38, mm10, rn5 and dm6. This needs to be done only once per assembly. 
+```R
+gtf2sqlite(assembly = "hg19", db.file="data/human_hg19_ens75_txdb.sqlite")
+```
+### Extract features from the database
+List of features returned by `loadAnnotation()` will be used to annotate circRNAs. Saving it as a separate object is a good practice once we start analyzing multiple circRNA libraries.
+```R
+annot.list <- loadAnnotation("data/human_hg19_ens75_txdb.sqlite")
+```
+### Load and annotate circRNAs
+```R
+circs.f <- annotateCircs(circs.bed = "data/Sy5y_D0_sites.bed", annot.list = annot.list, assembly = "hg19")
+```
+### Plot data
+```R
+circHist(circs.f, 0.5)
+annotPie(circs.f, 0.02)
+```

tests/simple/test_load_data.R

@@ -1,5 +1,7 @@
 
-annot.list <- loadAnnotation("data/hsa_GRCh37_ens75.sqlite")
+gtf2sqlite(assembly = "hg19", db.file="data/test.sqlite")
+
+annot.list <- loadAnnotation("data/test.sqlite")
 
 circs.f <- annotateCircs(circs.bed = "data/Sy5y_D0_sites.bed", annot.list = annot.list, assembly = "hg19")