Package: RCAS 1.31.0

Bora Uyar

RCAS: RNA Centric Annotation System

RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5'/3' UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses and discriminative motif discovery.

Authors:Bora Uyar [aut, cre], Dilmurat Yusuf [aut], Ricardo Wurmus [aut], Altuna Akalin [aut]

RCAS_1.31.0.tar.gz
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RCAS.pdf |RCAS.html✨
RCAS/json (API)
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Peer review:

On BioConductor:RCAS-1.31.0(bioc 3.20)RCAS-1.30.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

40 exports 1.51 score 152 dependencies 1 dependents 8 mentions

Last updated 2 months agofrom:12f9502dfc

Exports:calculateCoverageProfilecalculateCoverageProfileFromTxdbcalculateCoverageProfileListcalculateCoverageProfileListFromTxdbcheckSeqDbcreateControlRegionscreateDBcreateOrthologousGeneSetListdeleteSampleDataFromDBdiscoverFeatureSpecificMotifsextractSequencesfindDifferentialMotifsfindEnrichedFunctionsgenerateKmersgetFeatureBoundaryCoveragegetFeatureBoundaryCoverageBingetFeatureBoundaryCoverageMultigetIntervalOverlapMatrixgetMotifSummaryTablegetPWMgetTargetedGenesTablegetTxdbFeaturesgetTxdbFeaturesFromGRangesimportBedimportBedFilesimportGtfparseMsigdbplotFeatureBoundaryCoverageprintMsigdbDatasetqueryGffretrieveOrthologsrunGSEArunMotifDiscoveryrunMotifRGrunReportrunReportMetaAnalysisrunTopGOsummarizeDatabaseContentsummarizeQueryRegionssummarizeQueryRegionsMulti

Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg19bslibcachemclicliprcodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrDTevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsgenomationGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegprofiler2gridBasegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2imputeIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpbapplypheatmappillarpkgconfigplogrplotlyplotrixplyrpngprettyunitsprogresspromisesproxypurrrR6rangerrappdirsRColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesseqLogoseqPatternsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc