DOI: 10.18129/B9.bioc.epigraHMM  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see epigraHMM.

Epigenomic R-based analysis with hidden Markov models

Bioconductor version: 3.16

epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

Author: Pedro Baldoni [aut, cre]

Maintainer: Pedro Baldoni <pedrobaldoni at gmail.com>

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HTML R Script Consensus and Differential Peak Calling With epigraHMM
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biocViews ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, HiddenMarkovModel, Software
Version 1.6.4
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License MIT + file LICENSE
Depends R (>= 3.5.0)
Imports Rcpp, magrittr, data.table, SummarizedExperiment, methods, GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices
LinkingTo Rcpp, RcppArmadillo, Rhdf5lib
Suggests testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData
SystemRequirements GNU make
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package epigraHMM_1.6.4.tar.gz
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