Package: DegCre 1.8.0

Brian S. Roberts

DegCre: Probabilistic association of DEGs to CREs from differential data

DegCre generates associations between differentially expressed genes (DEGs) and cis-regulatory elements (CREs) based on non-parametric concordance between differential data. The user provides GRanges of DEG TSS and CRE regions with differential p-value and optionally log-fold changes and DegCre returns an annotated Hits object with associations and their calculated probabilities. Additionally, the package provides functionality for visualization and conversion to other formats.

Authors:Brian S. Roberts [aut, cre]

DegCre_1.8.0.tar.gz
DegCre_1.8.0.zip(r-4.7)DegCre_1.8.0.zip(r-4.6)DegCre_1.8.0.zip(r-4.5)
DegCre_1.8.0.tgz(r-4.6-any)DegCre_1.8.0.tgz(r-4.5-any)
DegCre_1.8.0.tar.gz(r-4.7-any)DegCre_1.8.0.tar.gz(r-4.6-any)
DegCre_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DegCre/json (API)
NEWS

# Install 'DegCre' in R:
install.packages('DegCre', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/briansroberts/degcre/issues

Datasets:
  • DexNR3C1 - DegCre input data for examples.

On BioConductor:DegCre-1.9.0(bioc 3.24)DegCre-1.8.0(bioc 3.23)

geneexpressiongeneregulationatacseqchipseqdnaseseqrnaseq

4.88 score 5 stars 3 scripts 256 downloads 17 exports 110 dependencies

Last updated from:849d519bfc (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE355
linux-devel-x86_64NOTE640
source / vignettesOK450
linux-release-x86_64NOTE629
macos-release-arm64NOTE376
macos-oldrel-arm64NOTE291
windows-develNOTE826
windows-releaseNOTE803
windows-oldrelNOTE720
wasm-releaseOK299

Exports:calcAssocProbORcalcRawAssocProbORchangeColorAlphacollapseDegCreToGeneconvDegCreResListToCreGeneScoreGRconvertDegCreDataFrameconvertdegCreResListToGInteractiondegCrePRAUCgetAssocDistHitsgetDistBinNullAssocProbgetExpectAssocPerDEGoptimizeAlphaDegCreplotBrowserDegCreplotDegCreAssocProbVsDistplotDegCreBinHeuristicplotExpectedAssocsPerDegrunDegCre

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydigestdir.expirydplyrfarverfastmapfilelockformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggplotifygluegridGraphicsgtablehttrInteractionSetIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpillarpkgconfigplotgardenerplyrplyrangespngpurrrqvalueR6rappdirsRColorBrewerRcppRCurlreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyselectTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlyulab.utils

DegCre Introduction and Examples

Brian S. Roberts

Rendered fromdegcre_introduction_and_examples.Rmdusingknitr::rmarkdownon Jun 07 2026.

Last update: 2024-08-22
Started: 2023-10-03