Convert between DESeqDataSet and DGEList objects | DGEList to DESeqDataSet | DESeqDataSet to DGEList | Create DGEList objects from SummarizedExperiment | FAQ | Coerce DGEList to RangedSummarizedExperiment | Session info
Package: DEFormats 1.41.0
Andrzej Oleś
DEFormats: Differential gene expression data formats converter
Convert between different data formats used by differential gene expression analysis tools.
Authors:
DEFormats_1.41.0.tar.gz
DEFormats_1.41.0.zip(r-4.7)DEFormats_1.41.0.zip(r-4.6)DEFormats_1.41.0.zip(r-4.5)
DEFormats_1.41.0.tgz(r-4.6-any)DEFormats_1.41.0.tgz(r-4.5-any)
DEFormats_1.41.0.tar.gz(r-4.7-any)DEFormats_1.41.0.tar.gz(r-4.6-any)
DEFormats_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DEFormats/json (API)
| # Install 'DEFormats' in R: |
| install.packages('DEFormats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/aoles/deformats/issues
On BioConductor:DEFormats-1.41.0(bioc 3.24)DEFormats-1.40.0(bioc 3.23)
immunooncologydifferentialexpressiongeneexpressionrnaseqsequencingtranscription
Last updated from:6052e65b86. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 192 | ||
| linux-devel-x86_64 | NOTE | 311 | ||
| source / vignettes | OK | 247 | ||
| linux-release-x86_64 | NOTE | 294 | ||
| macos-release-arm64 | NOTE | 142 | ||
| macos-oldrel-arm64 | NOTE | 166 | ||
| windows-devel | NOTE | 221 | ||
| windows-release | NOTE | 220 | ||
| windows-oldrel | NOTE | 231 | ||
| wasm-release | OK | 167 |
Exports:as.DESeqDataSetas.DGEListDGEListsimulateNormFactorssimulateRnaSeqData
Dependencies:abindbackportsBHBiobaseBiocGenericsBiocParallelcheckmateclicodetoolscpp11data.tableDelayedArrayDESeq2edgeRfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsR6RColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodSummarizedExperimentvctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert to DESeqDataSet | as.DESeqDataSet as.DESeqDataSet.DGEList |
| Convert to DGEList | as.DGEList as.DGEList.DESeqDataSet |
| Convert Between Differential Gene Expression Data Formats | DEFormats |
| DGEList Constructor Generic | DGEList DGEList,RangedSummarizedExperiment-method |
| Simulate Normalization Factors | simulateNormFactors |
| Example counts table of RNA-seq data | simulateRnaSeqData |
