RCAS: RNA Centric Annotation System

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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.

Author
Bora Uyar [aut, cre], Dilmurat Yusuf [aut], Ricardo Wurmus [aut], Altuna Akalin [aut]
Date of publication
None
Maintainer
Bora Uyar <bora.uyar@mdc-berlin.de>
License
Artistic-2.0
Version
1.0.0

View on Bioconductor

Man pages

calculateCoverageProfile
calculateCoverageProfile
calculateCoverageProfileFromTxdb
calculateCoverageProfileFromTxdb
calculateCoverageProfileList
calculateCoverageProfileList
calculateCoverageProfileListFromTxdb
calculateCoverageProfileListFromTxdb
createControlRegions
createControlRegions
createOrthologousGeneSetList
createOrthologousMsigdbDataset
extractSequences
extractSequences
geneSets
Random test gene sets
getFeatureBoundaryCoverage
getFeatureBoundaryCoverage
getFeatureBoundaryCoverageBin
getFeatureBoundaryCoverageBin
getMotifSummaryTable
getMotifSummaryTable
getTargetedGenesTable
getTargetedGenesTable
getTxdbFeatures
getTxdbFeatures
getTxdbFeaturesFromGRanges
getTxdbFeaturesFromGRanges
gff
Sample GFF file imported as a GRanges object
importBed
importBed
importGtf
importGtf
parseMsigdb
parseMsigdb
printMsigdbDataset
Print MSIGDB Dataset to a file This function is used to print...
queryGff
queryGff
queryRegions
Sample BED file imported as a GRanges object
retrieveOrthologs
retrieveOrthologs
runGSEA
runGSEA
runMotifRG
runMotifRG
runReport
Generate a RCAS Report for a list of transcriptome-level...
runTopGO
runTopGO
summarizeQueryRegions
summarizeQueryRegions

Files in this package

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