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✨
DESCRIPTION |NEWS
card.svg |card.png
epiRomics/json (API)

# 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)

epigenetics chipseq atacseq rnaseq visualization sequencing software histonemodification generegulation transcription functionalgenomics atac-seq chip-seq chromatin-accessibiity data-visualization enhancer enhancer-prediction epigenomics histone multi-omics regulatory-network regulome-analysis rna-seq transcription-factor-binding transcription-factors ucsc-browser

5.86 score 5 stars 41 scripts 60 exports 168 dependencies

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

Target	Result	Time
bioc-checks	NOTE	357
linux-devel-x86_64	OK	618
source / vignettes	OK	546
linux-release-x86_64	OK	616
macos-release-arm64	OK	556
macos-oldrel-arm64	OK	325
windows-devel	ERROR	481
windows-release	ERROR	451
windows-oldrel	ERROR	478
wasm-release	OK	337

Exports:analyze_tf_cobinding analyze_tf_overlap annotate_enhancers annotations annotations<-benchmark_enhancer_predictor build_database cache_data call_accessible_regions chromatin_state_categories classify_celltype_accessibility classify_chromatin_states epiRomics_annotate_putative epiRomics_build_dB epiRomics_cache_data epiRomics_cache_path epiRomics_chromatin_states epiRomics_chromatin_states_categories epiRomics_enhanceosome epiRomics_enhancer_predictor_to_ref epiRomics_enhancers_co_marks epiRomics_enhancers_filter epiRomics_filter_accessible epiRomics_has_cache epiRomics_putative_enhancers epiRomics_quick_view epiRomics_regions_of_interest epiRomics_tf_cobinding epiRomics_tf_overlap epiRomics_track_layer epiRomics_track_layer_fast epiRomics_track_layer_gene epiRomicsS4 filter_accessible_regions filter_enhancers find_enhanceosomes find_enhancers_by_comarks find_putative_enhancers genome genome<-get_cache_path get_regions_of_interest has_cache make_example_bigwig make_example_database make_example_enhanceosome make_example_putative_enhancers maxCovBwCached maxCovFilesCached meta meta<-organism organism<-plot_gene_tracks plot_quick_view plot_signal_histogram plot_tracks plot_tracks_fast txdb txdb<-

Dependencies:abind AnnotationDbi AnnotationHub annotatr ape aplot askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob boot BSgenome bslib cachem caTools ChIPseeker cigarillo cli clipr cluster codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray digest DOSE dplyr enrichit enrichplot evaluate farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim gplots gridGraphics gtable gtools highr hms htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl patchwork pillar pkgconfig plotrix plyr png polyclip prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RCurl readr regioneR reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML XVector yaml yulab.utils

Getting Started with epiRomics

Rendered fromgetting-started-with-epiRomics.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
epiRomics: Epigenomic Analysis Package Built for R (epiRomics)	epiRomics-package epiRomics
Analyze statistical significance of TF co-binding at enhanceosome regions	analyze_tf_cobinding
Analyze pairwise and multi-way overlap between transcription factor binding sites	analyze_tf_overlap
Annotate putative enhancers with functional database overlaps	annotate_enhancers
Access the genomic annotations slot of an epiRomicsS4 object	annotations annotations,epiRomicsS4-method
Replace the annotations slot of an epiRomicsS4 object	annotations-set annotations<- annotations<-,epiRomicsS4-method
Evaluate histone marks against any curated reference database	benchmark_enhancer_predictor
Build epiRomics database	build_database
Download and Cache epiRomics Example Data	cache_data
Compute per-region signal z-scores from a BigWig file	call_accessible_regions
Return chromatin state category definitions	chromatin_state_categories
Classify regions by cell-type-specific binary accessibility	classify_celltype_accessibility
Classify genomic regions by histone chromatin state with genomic context	classify_chromatin_states
Accessors for the epiRomicsS4 class	epiRomicsS4-accessors
An S4 class to manage epiRomics databases and downstream results	epiRomicsS4 epiRomicsS4-class
Filter putative enhancers by chromatin accessibility evidence	filter_accessible_regions
Filters putative enhancers called by epiRomics_enhancers by crossing against curated FANTOM data	filter_enhancers
Identifies putative enhanceosome regions by cross-referencing candidate enhancer regions against co-TF enrichment	find_enhanceosomes
Identifies putative enhancer regions utilizing select histone mark co-occurrence	find_enhancers_by_comarks
Identify putative enhancer regions using rule-based histone logic	find_putative_enhancers
Access the genome assembly name	genome genome,epiRomicsS4-method
Replace the genome assembly name	genome-set genome<- genome<-,epiRomicsS4-method
Get Path to Cached epiRomics Data (No Download)	get_cache_path
Define regions of interest and filter enhanceosome by overlap	get_regions_of_interest
Check Whether epiRomics Example Data is Cached	has_cache
Create a temporary synthetic BigWig file for use in examples	make_example_bigwig
Build a synthetic epiRomicsS4 database for use in examples	make_example_database
Build a synthetic enhanceosome result for use in examples	make_example_enhanceosome
Build a synthetic putative-enhancer result for use in examples	make_example_putative_enhancers
BigWig coverage calculation	maxCovBwCached
Multiple BigWig coverage calculation	maxCovFilesCached
Access the metadata slot of an epiRomicsS4 object	meta meta,epiRomicsS4-method
Replace the metadata slot of an epiRomicsS4 object	meta-set meta<- meta<-,epiRomicsS4-method
Access the organism annotation package name	organism organism,epiRomicsS4-method
Replace the organism annotation package name	organism-set organism<- organism<-,epiRomicsS4-method
Visualize any gene locus with multi-track BigWig overlay	plot_gene_tracks
Quick standalone gene/region visualization from BigWig files	plot_quick_view
Plot signal distribution histogram for accessibility threshold selection	plot_signal_histogram
Multi-track genomic visualization (base R graphics)	plot_tracks plot_tracks_fast
Access the TxDb package::object identifier slot	txdb txdb,epiRomicsS4-method
Replace the TxDb identifier slot of an epiRomicsS4 object	txdb-set txdb<- txdb<-,epiRomicsS4-method