Package: derfinder 1.41.0
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_1.41.0.tar.gz
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derfinder.pdf |derfinder.html✨
derfinder/json (API)
NEWS
| # Install 'derfinder' in R: |
| install.packages('derfinder', repos = c('https://bioc.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-1.39.0(bioc 3.20)derfinder-1.38.0(bioc 3.19)
differentialexpressionsequencingrnaseqchipseqdifferentialpeakcallingsoftwareimmunooncologycoverageannotation-agnosticbioconductorderfinder
Last updated 23 days agofrom:216267d650. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | ERROR | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | ERROR | Oct 31 2024 |
Exports:advancedArganalyzeChrannotateRegionscalculatePvaluescalculateStatscoerceGRcollapseFullCoveragecoverageToExoncreateBwcreateBwSampledefine_clusterextendedMapSeqlevelsfilterDatafindRegionsfullCoveragegetRegionCoveragegetTotalMappedloadCoveragemakeGenomicStatemakeModelsmergeResultspreprocessCoveragerailMatrixrawFilesregionMatrixsampleDepth
Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibbumphuntercachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayderfinderHelperdigestdoRNGevaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplyrpngqvalueR6rappdirsRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc
