Package: consensusDE 1.25.0

Ashley J. Waardenberg

consensusDE: RNA-seq analysis using multiple algorithms

This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation.

Authors:Ashley J. Waardenberg [aut, cre], Martha M. Cooper [ctb]

consensusDE_1.25.0.tar.gz
consensusDE_1.25.0.zip(r-4.5)consensusDE_1.25.0.zip(r-4.4)consensusDE_1.25.0.zip(r-4.3)
consensusDE_1.25.0.tgz(r-4.4-any)consensusDE_1.25.0.tgz(r-4.3-any)
consensusDE_1.25.0.tar.gz(r-4.5-noble)consensusDE_1.25.0.tar.gz(r-4.4-noble)
consensusDE_1.25.0.tgz(r-4.4-emscripten)consensusDE_1.25.0.tgz(r-4.3-emscripten)
consensusDE.pdf |consensusDE.html✨
consensusDE/json (API)
NEWS

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

Peer review:

On BioConductor:consensusDE-1.25.0(bioc 3.21)consensusDE-1.24.0(bioc 3.20)

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

transcriptomicsmultiplecomparisonclusteringsequencingsoftware

4.00 score 10 scripts 170 downloads 1 mentions 3 exports 140 dependencies

Last updated 2 months agofrom:44f18e03c1. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:buildSummarizeddiag_plotsmulti_de_pairs

Dependencies:abindairwayAnnotationDbiAnnotationFilteraroma.lightaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdendextendDESeq2digestdplyrEDASeqedgeREnsDb.Hsapiens.v86ensembldbfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehmshttrhttr2hwriterinterpIRangesisobandjpegjsonliteKEGGRESTlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpcaMethodspillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerRUVSeqS4ArraysS4VectorsscalesShortReadsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectTxDb.Dmelanogaster.UCSC.dm3.ensGeneUCSC.utilsutf8vctrsviridisviridisLitewithrXMLxml2XVectoryamlzlibbioc

consensusDE: DE analysis using multiple algorithms

Ashley J. Waardenberg

Rendered fromconsensusDE.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2019-12-03
Started: 2018-09-28