Package: epiregulon 1.3.6

Xiaosai Yao

epiregulon: Gene regulatory network inference from single cell epigenomic data

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

Authors:Xiaosai Yao [aut, cre], Tomasz Włodarczyk [aut], Aaron Lun [aut], Shang-Yang Chen [aut]

epiregulon_1.3.6.tar.gz
epiregulon_1.3.6.zip(r-4.5)epiregulon_1.3.6.zip(r-4.4)
epiregulon_1.3.6.tgz(r-4.5-x86_64)epiregulon_1.3.6.tgz(r-4.5-arm64)epiregulon_1.3.6.tgz(r-4.4-x86_64)epiregulon_1.3.6.tgz(r-4.4-arm64)
epiregulon_1.3.6.tar.gz(r-4.5-noble)epiregulon_1.3.6.tar.gz(r-4.4-noble)
epiregulon_1.3.6.tgz(r-4.4-emscripten)
epiregulon.pdf |epiregulon.html
epiregulon/json (API)
NEWS

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

Bug tracker:https://github.com/xiaosaiyao/epiregulon/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:epiregulon-1.3.5(bioc 3.21)epiregulon-1.2.0(bioc 3.20)

singlecellgeneregulationnetworkinferencenetworkgeneexpressiontranscriptiongenetargetcpp

6.67 score 14 stars 17 scripts 163 downloads 11 exports 192 dependencies

Last updated 18 days agofrom:b201d70456. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 14 2025
R-4.5-win-x86_64NOTEMar 14 2025
R-4.5-mac-x86_64NOTEMar 14 2025
R-4.5-mac-aarch64NOTEMar 14 2025
R-4.5-linux-x86_64NOTEMar 14 2025
R-4.4-win-x86_64NOTEMar 14 2025
R-4.4-mac-x86_64NOTEMar 14 2025
R-4.4-mac-aarch64NOTEMar 14 2025
R-4.4-linux-x86_64NOTEMar 14 2025

Exports:addLogFCaddMotifScoreaddTFMotifInfoaddWeightsaggregateAcrossCellsaggregateAcrossCellsFastcalculateActivitycalculateP2GgetRegulongetTFMotifInfopruneRegulon

Dependencies:abindalabaster.basealabaster.matrixalabaster.schemasannotateAnnotationDbiAnnotationHubaskpassassortheadAUCellAzureAuthAzureGraphAzureRMRAzureStorbackportsbase64encbeachmatBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionBiostringsbitbit64bitopsblobblusterBSgenomeBSgenome.Hsapiens.UCSC.hg19BSgenome.Hsapiens.UCSC.hg38BSgenome.Mmusculus.UCSC.mm10bslibcachemcaToolscheckmatecliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngedgeRentropyevaluateExperimentHubfansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegraphGSEABasegtablegtoolsh5mreadHDF5ArrayhighrhtmltoolshtmlwidgetshttrigraphIRangesirlbaisobandjosejquerylibjsonlitejsonvalidateKEGGRESTkernlabknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimemixtoolsmotifmatchrMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigplogrplotlypngpromisespurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitersvdrtracklayerS4ArraysS4VectorssassScaledMatrixscalesscMultiomescranscuttlesegmentedseqLogoSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsysTFBSToolsTFMPvaluetibbletidyrtidyselecttinytexUCSC.utilsutf8uuidV8vctrsviridisLitewithrxfunXMLxml2xtableXVectoryaml

Epiregulon tutorial with MultiAssayExperiment

Rendered frommultiome.mae.Rmdusingknitr::rmarkdownon Mar 14 2025.

Last update: 2024-11-24
Started: 2022-09-12