Package: SEtools 1.21.0

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]

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SEtools.pdf |SEtools.html✨
SEtools/json (API)
NEWS

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

Peer review:

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

Datasets:
  • SE - Example dataset

On BioConductor:SEtools-1.21.0(bioc 3.21)SEtools-1.20.0(bioc 3.20)

geneexpression

5.63 score 2 stars 71 scripts 412 downloads 9 exports 118 dependencies

Last updated 3 months agofrom:17a95304cf. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 19 2025
R-4.5-winNOTEJan 19 2025
R-4.5-linuxNOTEJan 19 2025
R-4.4-winNOTEJan 19 2025
R-4.4-macNOTEJan 19 2025
R-4.3-winNOTEJan 19 2025
R-4.3-macNOTEJan 19 2025

Exports:aggSEcastSEflattenPBlog2FCmergeSEsresetAllSEtoolsOptionsse2xlssehmsvacor

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcacachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIDelayedArrayDESeq2digestdoParalleledgeRfansifarverfastmapforeachformatRfutile.loggerfutile.optionsgclusgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslopenxlsxpermutepheatmappillarpkgconfigplogrpngqapR6randomcoloRRColorBrewerRcppRcppArmadilloregistryrjsonrlangRSQLiteRtsneS4ArraysS4VectorsscalessechmseriationshapesnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvasystibbleTSPUCSC.utilsutf8V8vctrsveganviridisLitewithrXMLxtableXVectorzip

SEtools

Pierre-Luc Germain

Rendered fromSEtools.Rmdusingknitr::rmarkdownon Jan 19 2025.

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