Package: DEFormats 1.35.0

Andrzej Oleś

DEFormats: Differential gene expression data formats converter

Convert between different data formats used by differential gene expression analysis tools.

Authors:Andrzej Oleś

DEFormats_1.35.0.tar.gz
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DEFormats.pdf |DEFormats.html✨
DEFormats/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/aoles/deformats/issues

On BioConductor:DEFormats-1.35.0(bioc 3.21)DEFormats-1.34.0(bioc 3.20)

immunooncologydifferentialexpressiongeneexpressionrnaseqsequencingtranscription

6.82 score 4 stars 1 packages 78 scripts 429 downloads 1 mentions 5 exports 73 dependencies

Last updated 2 months agofrom:05370ad991. Checks:OK: 5 NOTE: 2. Indexed: yes.

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

Exports:as.DESeqDataSetas.DGEListDGEListsimulateNormFactorssimulateRnaSeqData

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelcheckmateclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDESeq2edgeRfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsscalessnowSparseArraystatmodSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Differential gene expression data formats converter

Andrzej Oleś

Rendered fromDEFormats.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2018-02-07
Started: 2016-03-23

Readme and manuals

Help Manual

Help pageTopics
Convert to DESeqDataSetas.DESeqDataSet as.DESeqDataSet.DGEList
Convert to DGEListas.DGEList as.DGEList.DESeqDataSet
Convert Between Differential Gene Expression Data FormatsDEFormats
DGEList Constructor GenericDGEList DGEList,RangedSummarizedExperiment-method
Simulate Normalization FactorssimulateNormFactors
Example counts table of RNA-seq datasimulateRnaSeqData