Package: SEtools 1.26.0

Pierre-Luc Germain

SEtools: SEtools: tools for working with SummarizedExperiment

This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).

Authors:Pierre-Luc Germain [cre, aut]

SEtools_1.26.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
SEtools/json (API)
NEWS

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

Bug tracker:https://github.com/plger/setools/issues

Datasets:
  • SE - Example dataset

On BioConductor:SEtools-1.27.0(bioc 3.24)SEtools-1.26.0(bioc 3.23)

geneexpression

6.22 score 3 stars 93 scripts 366 downloads 9 exports 111 dependencies

Last updated from:881d52854f (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR195
linux-devel-x86_64NOTE382
source / vignettesOK297
linux-release-x86_64NOTE349
macos-release-arm64NOTE180
macos-oldrel-arm64NOTE300
windows-develNOTE270
windows-releaseNOTE248
windows-oldrelNOTE328
wasm-releaseOK152

Exports:aggSEcastSEflattenPBlog2FCmergeSEsresetAllSEtoolsOptionsse2xlssehmsvacor

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcacachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIDelayedArrayDESeq2digestdoParalleledgeRfarverfastmapforeachformatRfutile.loggerfutile.optionsgclusgenefiltergenericsGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslopenxlsxpermutepheatmappkgconfigpngqapR6randomcoloRRColorBrewerRcppRcppArmadilloregistryrjsonrlangRSQLiteRtsneS4ArraysS4VectorsS7scalessechmSeqinfoseriationshapesnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvasysTSPV8vctrsveganviridisLitewithrXMLxtableXVectorzip

SEtools

Pierre-Luc Germain

Rendered fromSEtools.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-11-27
Started: 2019-06-15

Readme and manuals

Help Manual

Help pageTopics
aggSEaggSE
castSEcastSE
Example datasetdata SE
flattenPBflattenPB
log2FClog2FC
mergeSEsmergeSEs
resetAllSEtoolsOptionsresetAllSEtoolsOptions
se2xlsxse2xls
sehmsehm
svacorsvacor