Package: RiboDiPA 1.20.0

Ji-Ping Wang

RiboDiPA: Differential pattern analysis for Ribo-seq data

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

Authors:Keren Li [aut], Matt Hope [aut], Xiaozhong Wang [aut], Ji-Ping Wang [aut, cre]

RiboDiPA_1.20.0.tar.gz
RiboDiPA_1.20.0.zip(r-4.7)RiboDiPA_1.20.0.zip(r-4.6)RiboDiPA_1.20.0.zip(r-4.5)
RiboDiPA_1.20.0.tgz(r-4.6-x86_64)RiboDiPA_1.20.0.tgz(r-4.6-arm64)RiboDiPA_1.20.0.tgz(r-4.5-x86_64)RiboDiPA_1.20.0.tgz(r-4.5-arm64)
RiboDiPA_1.20.0.tar.gz(r-4.7-arm64)RiboDiPA_1.20.0.tar.gz(r-4.7-x86_64)RiboDiPA_1.20.0.tar.gz(r-4.6-arm64)RiboDiPA_1.20.0.tar.gz(r-4.6-x86_64)
RiboDiPA_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RiboDiPA/json (API)
NEWS

# Install 'RiboDiPA' in R:
install.packages('RiboDiPA', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • data.binned - An example of binned P-sites data
  • data.psite - An example of P-site coverage data
  • result.exon - An example of exon-level differential pattern analysis result
  • result.pst - An example of differential pattern analysis result

On BioConductor:RiboDiPA-1.21.0(bioc 3.24)RiboDiPA-1.20.0(bioc 3.23)

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

riboseqgeneexpressiongeneregulationdifferentialexpressionsequencingcoveragealignmentrnaseqimmunooncologyqualitycontroldataimportsoftwarenormalizationcpp

4.00 score 1 scripts 351 downloads 12 exports 136 dependencies

Last updated from:5fc14f670b (on RELEASE_3_23). Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR235
linux-devel-arm64NOTE678
linux-devel-x86_64NOTE830
source / vignettesOK527
linux-release-arm64NOTE646
linux-release-x86_64NOTE756
macos-release-arm64NOTE428
macos-release-x86_64NOTE881
macos-oldrel-arm64NOTE406
macos-oldrel-x86_64NOTE941
windows-develNOTE730
windows-releaseNOTE638
windows-oldrelNOTE734
wasm-releaseOK190

Exports:binTrackbpTrackdataBinningdiffPatternTestdiffPatternTestExonexonTracknormFactorplotTestplotTrackpsiteCalpsiteMappingRiboDiPA

Dependencies:abindAnnotationDbiaskpassbackportsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcallrcheckmatecigarilloclicodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydensEstBayesdescDESeq2distributionaldoParalleldplyrelitismfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehmshttrhttr2inlineIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitloomagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmenumDerivopensslpillarpkgbuildpkgconfigplyrpngposteriorprettyunitsprocessxprogresspspurrrQuickJSRqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRCurlreldistreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLiterstanrstantoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArrayStanHeadersstringistringrSummarizedExperimentsystensorAtibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryaml

RiboDiPA R package

Keren Li, Matthew Hope, Xiaozhong A. Wang, Ji-Ping Wang

Rendered fromRiboDiPA.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-12-29
Started: 2020-04-20