Basics | Install r Biocpkg('derfinder') | Required knowledge | Asking for help | Citing r Biocpkg('derfinder') | Quick start to using to r Biocpkg('derfinder') | Introduction | Sample DER Finder analysis | Reproducibility | Bibliography
Package: derfinder 1.47.0
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_1.47.0.tar.gz
derfinder_1.47.0.zip(r-4.7)derfinder_1.47.0.zip(r-4.6)derfinder_1.47.0.zip(r-4.5)
derfinder_1.47.0.tgz(r-4.6-any)derfinder_1.47.0.tgz(r-4.5-any)
derfinder_1.47.0.tar.gz(r-4.7-any)derfinder_1.47.0.tar.gz(r-4.6-any)
derfinder_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
derfinder/json (API)
| # 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
Datasets:
- 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:ab0f068105. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 285 | ||
| linux-devel-x86_64 | NOTE | 615 | ||
| source / vignettes | OK | 474 | ||
| linux-release-x86_64 | NOTE | 628 | ||
| macos-release-arm64 | NOTE | 435 | ||
| macos-oldrel-arm64 | NOTE | 361 | ||
| windows-devel | NOTE | 510 | ||
| windows-release | NOTE | 523 | ||
| windows-oldrel | NOTE | 533 | ||
| wasm-release | OK | 258 |
Exports:advancedArganalyzeChrannotateRegionscalculatePvaluescalculateStatscoerceGRcollapseFullCoveragecoverageToExoncreateBwcreateBwSampledefine_clusterextendedMapSeqlevelsfilterDatafindRegionsfullCoveragegetRegionCoveragegetTotalMappedloadCoveragemakeGenomicStatemakeModelsmergeResultspreprocessCoveragerailMatrixrawFilesregionMatrixsampleDepth
Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibbumphuntercachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayderfinderHelperdigestdoRNGevaluatefarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigplyrpngqvalueR6rappdirsRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml
derfinder quick start guide
Last update: 2025-07-22
Started: 2015-12-09
derfinder users guide
Asking for help | r Biocpkg('derfinder') users guide | Expressed regions-level | regionMatrix() | railMatrix() | Single base-level F-statistics | Example data | Phenotype data | Load the data | Filter coverage | Expressed region-level analysis | Via regionMatrix() | Find DERs with r Biocpkg('DESeq2') | Find DERs with r Biocpkg('limma') | Via railMatrix() | Single base-level F-statistics analysis | Models | Find candidate DERs | Explore results | optionStats | coveragePrep | fstats | regions | Nearest annotation | Time spent | Merge results | optionsMerge | fullRegions | fullAnnotatedRegions | ChIP-seq differential binding | Visually explore results | Interactive HTML reports | Miscellaneous features | Feature level analysis | Compare results visually | Export coverage to BigWig files | Advanced arguments | Non-human data | Functions that use multiple cores | Loading data details | Controlling loading from BAM files | Unfiltered base-level coverage | Input files in a different naming style | Loading data in chunks | Large number of samples | Flow charts | DER analysis flow chart | analyzeChr() flow chart | regionMatrix() flow chart | Base-level F-statistics projects | File organization | bash scripts | derfinder-analysis.R | derAnalysis.sh | Expressed regions-level projects | Summary | Reproducibility | Bibliography
Last update: 2024-12-12
Started: 2015-11-11
