Package: RiboDiPA 1.15.0

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_1.15.0.tar.gz
RiboDiPA_1.15.0.zip(r-4.5)RiboDiPA_1.15.0.zip(r-4.4)RiboDiPA_1.15.0.zip(r-4.3)
RiboDiPA_1.15.0.tgz(r-4.4-x86_64)RiboDiPA_1.15.0.tgz(r-4.4-arm64)RiboDiPA_1.15.0.tgz(r-4.3-x86_64)RiboDiPA_1.15.0.tgz(r-4.3-arm64)
RiboDiPA_1.15.0.tar.gz(r-4.5-noble)RiboDiPA_1.15.0.tar.gz(r-4.4-noble)
RiboDiPA_1.15.0.tgz(r-4.4-emscripten)RiboDiPA_1.15.0.tgz(r-4.3-emscripten)
RiboDiPA.pdf |RiboDiPA.html✨
RiboDiPA/json (API)
NEWS

# Install 'RiboDiPA' in R:
install.packages('RiboDiPA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.15.0(bioc 3.21)RiboDiPA-1.14.0(bioc 3.20)

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

riboseqgeneexpressiongeneregulationdifferentialexpressionsequencingcoveragealignmentrnaseqimmunooncologyqualitycontroldataimportsoftwarenormalization

4.18 score 1 scripts 147 downloads 12 exports 140 dependencies

Last updated 23 days agofrom:6225daff59. Checks:OK: 1 WARNING: 6 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-win-x86_64WARNINGNov 07 2024
R-4.5-linux-x86_64WARNINGNov 07 2024
R-4.4-win-x86_64WARNINGNov 07 2024
R-4.4-mac-x86_64WARNINGNov 07 2024
R-4.4-mac-aarch64NOTENov 07 2024
R-4.3-win-x86_64WARNINGNov 07 2024
R-4.3-mac-x86_64WARNINGNov 07 2024
R-4.3-mac-aarch64NOTENov 07 2024

Exports:binTrackbpTrackdataBinningdiffPatternTestdiffPatternTestExonexonTracknormFactorplotTestplotTrackpsiteCalpsiteMappingRiboDiPA

Dependencies:abindAnnotationDbiaskpassbackportsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcallrcheckmateclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydensEstBayesdescDESeq2digestdistributionaldoParalleldplyrelitismfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehmshttrhttr2inlineIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitloomagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmenumDerivopensslpillarpkgbuildpkgconfigplogrplyrpngposteriorprettyunitsprocessxprogresspspurrrQuickJSRqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRCurlreldistreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLiterstanrstantoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArrayStanHeadersstringistringrSummarizedExperimentsystensorAtibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryamlzlibbioc

RiboDiPA R package

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

Rendered fromRiboDiPA.Rmdusingknitr::rmarkdownon Nov 07 2024.

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