epiRomics
Epigenomic Analysis Package Built for R (epiRomics)
Bioconductor version: 3.23 · Package version: 1.0.0
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 <ammawla@ucdavis.edu> for suggestions, feedback, or bug reporting.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("epiRomics")Details
| Maintainer | Alex M. Mawla <ammawla@ucdavis.edu> |
| Author | Alex M. Mawla [aut, cre] (ORCID: <https://orcid.org/0000-0003-0907-464X>), Mark O. Huising [aut] (ORCID: <https://orcid.org/0000-0002-6594-2205>) |
| License | Artistic-2.0 |
| URL | https://huising-lab.github.io/epiRomics/, https://github.com/Huising-Lab/epiRomics |
| Bug Reports | https://github.com/Huising-Lab/epiRomics/issues |
| Downloads rank | 41 |
| Source branch | RELEASE_3_23 |
| biocViews | ATACSeq, ChIPSeq, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, RNASeq, Sequencing, Software, Transcription, Visualization |
Documentation
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Dependencies
Depends: R (>= 4.5.0)
Imports: AnnotationDbi (>= 1.68.0), annotatr (>= 1.32.0), BiocGenerics (>= 0.52.0), ChIPseeker (>= 1.42.0), data.table (>= 1.15.0), digest (>= 0.6.35), GenomeInfoDb (>= 1.42.0), GenomicFeatures (>= 1.58.0), GenomicRanges (>= 1.58.0), graphics, grDevices, IRanges (>= 2.40.0), methods, rtracklayer (>= 1.66.0), S4Vectors (>= 0.44.0), stats, tools, utils
Suggests: BiocFileCache (>= 2.14.0), knitr, org.Hs.eg.db (>= 3.20.0), org.Mm.eg.db (>= 3.20.0), parallel, rmarkdown, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.18.0), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.10.0)