Package: DEXSeq 1.53.0
Alejandro Reyes
DEXSeq: Inference of differential exon usage in RNA-Seq
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
Authors:
DEXSeq_1.53.0.tar.gz
DEXSeq_1.53.0.zip(r-4.5)DEXSeq_1.53.0.zip(r-4.4)DEXSeq_1.53.0.zip(r-4.3)
DEXSeq_1.53.0.tgz(r-4.4-any)DEXSeq_1.53.0.tgz(r-4.3-any)
DEXSeq_1.53.0.tar.gz(r-4.5-noble)DEXSeq_1.53.0.tar.gz(r-4.4-noble)
DEXSeq_1.53.0.tgz(r-4.4-emscripten)DEXSeq_1.53.0.tgz(r-4.3-emscripten)
DEXSeq.pdf |DEXSeq.html✨
DEXSeq/json (API)
NEWS
| # Install 'DEXSeq' in R: |
| install.packages('DEXSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:DEXSeq-1.53.0(bioc 3.21)DEXSeq-1.52.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysequencingrnaseqdifferentialexpressionalternativesplicingdifferentialsplicinggeneexpressionvisualization
Last updated 1 months agofrom:a6a6573114. Checks:OK: 2 ERROR: 1 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | OK | Nov 30 2024 |
| R-4.5-linux | ERROR | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:colData<-countsDEXSeqDEXSeqDataSetDEXSeqDataSetFromHTSeqDEXSeqDataSetFromSEDEXSeqHTMLDEXSeqResultsestimateDispersionsestimateExonFoldChangesestimateSizeFactorsexonIDsexonIDs<-featureCountsfeatureIDsfeatureIDs<-findOverlapsgeneIDsgeneIDs<-groupIDsgroupIDs<-perGeneQValueplotDEXSeqplotMAsampleAnnotationsubsetByOverlapstestForDEU
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArrayDESeq2digestdplyrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenefiltergeneplottergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehmshttrhttr2hwriterIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRhtslibrlangRsamtoolsRSQLiteS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxml2xtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Accessors for the 'counts' slot of a DEXSeqResults object. | counts counts,DEXSeqResults-method |
| Performs the differential exon usage test in a single command | DEXSeq |
| This functions are deprecated and will become defunct. | DEXSeq-defunct |
| DEXSeqDataSet object and constructors | DEXSeqDataSet DEXSeqDataSet-class DEXSeqDataSetFromHTSeq DEXSeqDataSetFromSE |
| Subset and replacements of DEXSeqDataSet slots | $<-,DEXSeqDataSet-method colData<-,DEXSeqDataSet,DataFrame-method [,DEXSeqDataSet,ANY,ANY,ANY-method [,DEXSeqDataSet,ANY,ANY-method [,DEXSeqDataSet,ANY-method [,DEXSeqDataSet-method |
| DEXSeq HTML report writer | DEXSeqHTML |
| DEXSeqResults object | DEXSeqResults DEXSeqResults-class |
| Estimate the dispersions for a DEXSeqDataSet | estimateDispersions estimateDispersions,DEXSeqDataSet-method |
| Estimates exon usage coefficients from the fitted terms of the GLM. | estimateExonFoldChanges |
| Estimate the size factors for a DEXSeqDataSet | estimateSizeFactors estimateSizeFactors,DEXSeqDataSet-method |
| Accessor functions for DEXSeqDataSet details | exonIDs exonIDs<- featureCounts featureIDs featureIDs<- geneIDs geneIDs<- groupIDs groupIDs<- sampleAnnotation |
| Methods from GRanges overlaps for the DEXSeq object | findOverlaps findOverlaps,DEXSeqResults,GenomicRanges-method findOverlaps-methods subsetByOverlaps subsetByOverlaps,DEXSeqResults,GenomicRanges-method subsetByOverlaps-methods |
| Summarize per-exon p-values into per-gene q-values. | perGeneQValue |
| Visualization of the per gene DEXSeq results. | plotDEXSeq |
| Plot dispersion estimates | plotDispEsts plotDispEsts,DEXSeqDataSet-method |
| Generate an MA plot | plotMA plotMA,DEXSeqDataSet-method plotMA,DEXSeqResults-method plotMA-methods |
| Test for Differential Exon Usage | testForDEU |
