Package: derfinder 1.46.0
Leonardo Collado-Torres
derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.
Authors:
derfinder_1.46.0.tar.gz
derfinder_1.46.0.zip(r-4.7)derfinder_1.46.0.zip(r-4.6)derfinder_1.46.0.zip(r-4.5)
derfinder_1.46.0.tgz(r-4.6-any)derfinder_1.46.0.tgz(r-4.5-any)
derfinder_1.46.0.tar.gz(r-4.7-any)derfinder_1.46.0.tar.gz(r-4.6-any)
derfinder_1.46.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
derfinder/json (API)
NEWS
| # Install 'derfinder' in R: |
| install.packages('derfinder', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lcolladotor/derfinder/issues
- genomeData - Genome samples processed data
- genomeDataRaw - Genome samples processed data
- genomeFstats - F-statistics for the example data
- genomeInfo - Genome samples information
- genomeRegions - Candidate DERs for example data
- genomicState - Genomic State for Hsapiens.UCSC.hg19.knownGene
On BioConductor:derfinder-1.47.0(bioc 3.24)derfinder-1.46.0(bioc 3.23)
differentialexpressionsequencingrnaseqchipseqdifferentialpeakcallingsoftwareimmunooncologycoverageannotation-agnosticbioconductorderfinder
Last updated from:b04edea04e (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 307 | ||
| linux-devel-x86_64 | NOTE | 664 | ||
| source / vignettes | OK | 455 | ||
| linux-release-x86_64 | NOTE | 690 | ||
| macos-release-arm64 | NOTE | 409 | ||
| macos-oldrel-arm64 | NOTE | 378 | ||
| windows-devel | NOTE | 539 | ||
| windows-release | NOTE | 549 | ||
| windows-oldrel | NOTE | 516 | ||
| wasm-release | OK | 216 |
Exports:advancedArganalyzeChrannotateRegionscalculatePvaluescalculateStatscoerceGRcollapseFullCoveragecoverageToExoncreateBwcreateBwSampledefine_clusterextendedMapSeqlevelsfilterDatafindRegionsfullCoveragegetRegionCoveragegetTotalMappedloadCoveragemakeGenomicStatemakeModelsmergeResultspreprocessCoveragerailMatrixrawFilesregionMatrixsampleDepth
Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibbumphuntercachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayderfinderHelperdigestdoRNGevaluatefarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigplyrpngqvalueR6rappdirsRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml
