Package: DegCre 1.3.0

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_1.3.0.tar.gz
DegCre_1.3.0.zip(r-4.5)DegCre_1.3.0.zip(r-4.4)DegCre_1.1.1.zip(r-4.3)
DegCre_1.3.0.tgz(r-4.4-any)DegCre_1.1.1.tgz(r-4.3-any)
DegCre_1.3.0.tar.gz(r-4.5-noble)DegCre_1.3.0.tar.gz(r-4.4-noble)
DegCre_1.3.0.tgz(r-4.4-emscripten)DegCre_1.1.1.tgz(r-4.3-emscripten)
DegCre.pdf |DegCre.html✨
DegCre/json (API)
NEWS

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

Peer review:

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

Datasets:
  • DexNR3C1 - DegCre input data for examples.

On BioConductor:DegCre-1.3.0(bioc 3.21)DegCre-1.2.0(bioc 3.20)

geneexpressiongeneregulationatacseqchipseqdnaseseqrnaseq

5.54 score 5 stars 2 scripts 132 downloads 17 exports 112 dependencies

Last updated 5 days agofrom:0bf14592a4. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 14 2024
R-4.5-winNOTEDec 14 2024
R-4.5-linuxNOTEDec 14 2024
R-4.4-winNOTEDec 14 2024
R-4.4-macNOTEDec 14 2024
R-4.3-winERRORSep 22 2024
R-4.3-macERRORSep 22 2024

Exports:calcAssocProbORcalcRawAssocProbORchangeColorAlphacollapseDegCreToGeneconvDegCreResListToCreGeneScoreGRconvertDegCreDataFrameconvertdegCreResListToGInteractiondegCrePRAUCgetAssocDistHitsgetDistBinNullAssocProbgetExpectAssocPerDEGoptimizeAlphaDegCreplotBrowserDegCreplotDegCreAssocProbVsDistplotDegCreBinHeuristicplotExpectedAssocsPerDegrunDegCre

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydigestdplyrfansifarverfastmapformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggplotifygluegridGraphicsgtablehttrInteractionSetIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpillarpkgconfigplogrplotgardenerplyrplyrangespngpurrrqvalueR6RColorBrewerRcppRCurlreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyselectTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlyulab.utilszlibbioc

DegCre Introduction and Examples

Brian S. Roberts

Rendered fromdegcre_introduction_and_examples.Rmdusingknitr::rmarkdownon Dec 14 2024.

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