Package: epiRomics 1.1.0

Alex M. Mawla

epiRomics: Epigenomic Analysis Package Built for R (epiRomics)

Integrates various levels of epigenomic information, including ChIP-seq, histone modification, ATAC-seq, and RNA-seq data. Regulatory network analysis uses combinatory approaches to infer regions of significance, such as enhancers. Downstream analysis identifies co-occurrence of epigenomic data at regions of interest. Visualization functions display multi-track genomic views with signal overlays. Please contact <[email protected]> for suggestions, feedback, or bug reporting.

Authors:Alex M. Mawla [aut, cre], Mark O. Huising [aut]

epiRomics_1.1.0.tar.gz
epiRomics_1.1.0.zip(r-4.7)epiRomics_1.1.0.zip(r-4.6)epiRomics_1.1.0.zip(r-4.5)
epiRomics_1.1.0.tgz(r-4.6-any)epiRomics_1.1.0.tgz(r-4.5-any)
epiRomics_1.1.0.tar.gz(r-4.7-any)epiRomics_1.1.0.tar.gz(r-4.6-any)
epiRomics_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
epiRomics/json (API)
NEWS

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

Bug tracker:https://github.com/huising-lab/epiromics/issues

Pkgdown/docs site:https://huising-lab.github.io

On BioConductor:epiRomics-1.1.0(bioc 3.24)epiRomics-1.0.0(bioc 3.23)

epigeneticschipseqatacseqrnaseqvisualizationsequencingsoftwarehistonemodificationgeneregulationtranscriptionfunctionalgenomicsatac-seqchip-seqchromatin-accessibiitydata-visualizationenhancerenhancer-predictionepigenomicshistonemulti-omicsregulatory-networkregulome-analysisrna-seqtranscription-factor-bindingtranscription-factorsucsc-browser

5.86 score 5 stars 41 scripts 154 downloads 60 exports 168 dependencies

Last updated from:9e2708e0bd. Checks:1 NOTE, 6 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE360
linux-devel-x86_64OK653
source / vignettesOK523
linux-release-x86_64OK623
macos-release-arm64OK376
macos-oldrel-arm64OK383
windows-develERROR394
windows-releaseERROR522
windows-oldrelERROR457
wasm-releaseOK320

Exports:analyze_tf_cobindinganalyze_tf_overlapannotate_enhancersannotationsannotations<-benchmark_enhancer_predictorbuild_databasecache_datacall_accessible_regionschromatin_state_categoriesclassify_celltype_accessibilityclassify_chromatin_statesepiRomics_annotate_putativeepiRomics_build_dBepiRomics_cache_dataepiRomics_cache_pathepiRomics_chromatin_statesepiRomics_chromatin_states_categoriesepiRomics_enhanceosomeepiRomics_enhancer_predictor_to_refepiRomics_enhancers_co_marksepiRomics_enhancers_filterepiRomics_filter_accessibleepiRomics_has_cacheepiRomics_putative_enhancersepiRomics_quick_viewepiRomics_regions_of_interestepiRomics_tf_cobindingepiRomics_tf_overlapepiRomics_track_layerepiRomics_track_layer_fastepiRomics_track_layer_geneepiRomicsS4filter_accessible_regionsfilter_enhancersfind_enhanceosomesfind_enhancers_by_comarksfind_putative_enhancersgenomegenome<-get_cache_pathget_regions_of_interesthas_cachemake_example_bigwigmake_example_databasemake_example_enhanceosomemake_example_putative_enhancersmaxCovBwCachedmaxCovFilesCachedmetameta<-organismorganism<-plot_gene_tracksplot_quick_viewplot_signal_histogramplot_tracksplot_tracks_fasttxdbtxdb<-

Dependencies:abindAnnotationDbiAnnotationHubannotatrapeaplotaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbootBSgenomebslibcachemcaToolsChIPseekercigarilloclicliprclustercodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestDOSEdplyrenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgplotsgridGraphicsgtablegtoolshighrhmshtmltoolshtmlwidgetshttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpatchworkpillarpkgconfigplotrixplyrpngpolyclipprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscatterpieSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLXVectoryamlyulab.utils

Getting Started with epiRomics

Alex M. Mawla & Mark O. Huising

Rendered fromgetting-started-with-epiRomics.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2026-04-20
Started: 2021-02-12

Readme and manuals

Help Manual

Help pageTopics
epiRomics: Epigenomic Analysis Package Built for R (epiRomics)epiRomics-package epiRomics
Analyze statistical significance of TF co-binding at enhanceosome regionsanalyze_tf_cobinding
Analyze pairwise and multi-way overlap between transcription factor binding sitesanalyze_tf_overlap
Annotate putative enhancers with functional database overlapsannotate_enhancers
Access the genomic annotations slot of an epiRomicsS4 objectannotations annotations,epiRomicsS4-method
Replace the annotations slot of an epiRomicsS4 objectannotations-set annotations<- annotations<-,epiRomicsS4-method
Evaluate histone marks against any curated reference databasebenchmark_enhancer_predictor
Build epiRomics databasebuild_database
Download and Cache epiRomics Example Datacache_data
Compute per-region signal z-scores from a BigWig filecall_accessible_regions
Return chromatin state category definitionschromatin_state_categories
Classify regions by cell-type-specific binary accessibilityclassify_celltype_accessibility
Classify genomic regions by histone chromatin state with genomic contextclassify_chromatin_states
Accessors for the epiRomicsS4 classepiRomicsS4-accessors
An S4 class to manage epiRomics databases and downstream resultsepiRomicsS4 epiRomicsS4-class
Filter putative enhancers by chromatin accessibility evidencefilter_accessible_regions
Filters putative enhancers called by epiRomics_enhancers by crossing against curated FANTOM datafilter_enhancers
Identifies putative enhanceosome regions by cross-referencing candidate enhancer regions against co-TF enrichmentfind_enhanceosomes
Identifies putative enhancer regions utilizing select histone mark co-occurrencefind_enhancers_by_comarks
Identify putative enhancer regions using rule-based histone logicfind_putative_enhancers
Access the genome assembly namegenome genome,epiRomicsS4-method
Replace the genome assembly namegenome-set genome<- genome<-,epiRomicsS4-method
Get Path to Cached epiRomics Data (No Download)get_cache_path
Define regions of interest and filter enhanceosome by overlapget_regions_of_interest
Check Whether epiRomics Example Data is Cachedhas_cache
Create a temporary synthetic BigWig file for use in examplesmake_example_bigwig
Build a synthetic epiRomicsS4 database for use in examplesmake_example_database
Build a synthetic enhanceosome result for use in examplesmake_example_enhanceosome
Build a synthetic putative-enhancer result for use in examplesmake_example_putative_enhancers
BigWig coverage calculationmaxCovBwCached
Multiple BigWig coverage calculationmaxCovFilesCached
Access the metadata slot of an epiRomicsS4 objectmeta meta,epiRomicsS4-method
Replace the metadata slot of an epiRomicsS4 objectmeta-set meta<- meta<-,epiRomicsS4-method
Access the organism annotation package nameorganism organism,epiRomicsS4-method
Replace the organism annotation package nameorganism-set organism<- organism<-,epiRomicsS4-method
Visualize any gene locus with multi-track BigWig overlayplot_gene_tracks
Quick standalone gene/region visualization from BigWig filesplot_quick_view
Plot signal distribution histogram for accessibility threshold selectionplot_signal_histogram
Multi-track genomic visualization (base R graphics)plot_tracks plot_tracks_fast
Access the TxDb package::object identifier slottxdb txdb,epiRomicsS4-method
Replace the TxDb identifier slot of an epiRomicsS4 objecttxdb-set txdb<- txdb<-,epiRomicsS4-method