RCAS: RNA Centric Annotation System

RCAS is an automated system that provides dynamic genome annotations for custom input files that contain transcriptomic regions. Such transcriptomic regions could be, for instance, peak regions detected by CLIP-Seq analysis that detect protein-RNA interactions, RNA modifications (alias the epitranscriptome), CAGE-tag locations, or any other collection of target regions at the level of the transcriptome. RCAS is designed as a reporting tool for the functional analysis of RNA-binding sites detected by high-throughput experiments. It takes as input a BED format file containing the genomic coordinates of the RNA binding sites and a GTF file that contains the genomic annotation features usually provided by publicly available databases such as Ensembl and UCSC. RCAS performs overlap operations between the genomic coordinates of the RNA binding sites and the genomic annotation features and produces in-depth annotation summaries such as the distribution of binding sites with respect to gene features (exons, introns, 5'/3' UTR regions, exon-intron boundaries, promoter regions, and whole transcripts). Moreover, by detecting the collection of targeted transcripts, RCAS can carry out functional annotation tables for enriched gene sets (annotated by the Molecular Signatures Database) and GO terms. As one of the most important questions that arise during protein-RNA interaction analysis; RCAS has a module for detecting sequence motifs enriched in the targeted regions of the transcriptome. A full interactive report in HTML format can be generated that contains interactive figures and tables that are ready for publication purposes.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RCAS")
AuthorBora Uyar [aut, cre], Dilmurat Yusuf [aut], Ricardo Wurmus [aut], Altuna Akalin [aut]
Bioconductor views Coverage GO GeneSetEnrichment GeneTarget GenomeAnnotation MotifAnnotation MotifDiscovery Software Transcriptomics
Date of publicationNone
MaintainerBora Uyar <bora.uyar@mdc-berlin.de>
LicenseArtistic-2.0
Version1.2.0

View on Bioconductor

Functions

calculateCoverageProfile Man page
calculateCoverageProfileFromTxdb Man page
calculateCoverageProfileList Man page
calculateCoverageProfileListFromTxdb Man page
createControlRegions Man page
createOrthologousGeneSetList Man page
extractSequences Man page
geneSets Man page
getFeatureBoundaryCoverage Man page
getFeatureBoundaryCoverageBin Man page
getMotifSummaryTable Man page
getTargetedGenesTable Man page
getTxdbFeatures Man page
getTxdbFeaturesFromGRanges Man page
gff Man page
importBed Man page
importGtf Man page
parseMsigdb Man page
plotFeatureBoundaryCoverage Man page
printMsigdbDataset Man page
queryGff Man page
queryRegions Man page
retrieveOrthologs Man page
runGSEA Man page
runMotifRG Man page
runReport Man page
runTopGO Man page
summarizeQueryRegions Man page

Files

DESCRIPTION
NAMESPACE
R
R/data.R R/enrichment_analysis.R R/motif_analysis.R R/plotting_functions.R R/report_functions.R
build
build/vignette.rds
data
data/datalist
data/geneSets.rda
data/gff.rda
data/queryRegions.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/RCAS.vignette.R
inst/doc/RCAS.vignette.Rmd
inst/doc/RCAS.vignette.html
inst/extdata
inst/extdata/msigdb_test.gmt
inst/extdata/testfile.bed
inst/reporting_scripts
inst/reporting_scripts/footer.html
inst/reporting_scripts/header.html
inst/reporting_scripts/report.Rmd
man
man/calculateCoverageProfile.Rd man/calculateCoverageProfileFromTxdb.Rd man/calculateCoverageProfileList.Rd man/calculateCoverageProfileListFromTxdb.Rd man/createControlRegions.Rd man/createOrthologousGeneSetList.Rd man/extractSequences.Rd man/geneSets.Rd man/getFeatureBoundaryCoverage.Rd man/getFeatureBoundaryCoverageBin.Rd man/getMotifSummaryTable.Rd man/getTargetedGenesTable.Rd man/getTxdbFeatures.Rd man/getTxdbFeaturesFromGRanges.Rd man/gff.Rd man/importBed.Rd man/importGtf.Rd man/parseMsigdb.Rd man/plotFeatureBoundaryCoverage.Rd man/printMsigdbDataset.Rd man/queryGff.Rd man/queryRegions.Rd man/retrieveOrthologs.Rd man/runGSEA.Rd man/runMotifRG.Rd man/runReport.Rd man/runTopGO.Rd man/summarizeQueryRegions.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/test_GO.R tests/testthat/test_data.R tests/testthat/test_motif.R tests/testthat/test_msigdb.R tests/testthat/test_report.R tests/testthat/test_txdbfeatures.R
vignettes
vignettes/RCAS.vignette.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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