DOI: 10.18129/B9.bioc.ALPS    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ALPS.

AnaLysis routines for ePigenomicS data

Bioconductor version: 3.10

The package provides analysis and publication quality visualization routines for genome-wide epigenomics data such as histone modification or transcription factor ChIP-seq, ATAC-seq, DNase-seq etc. The functions in the package can be used with any type of data that can be represented with bigwig files at any resolution. The goal of the ALPS is to provide analysis tools for most downstream analysis without leaving the R environment and most tools in the package require a minimal input that can be prepared with basic R, unix or excel skills.

Author: Venu Thatikonda, Natalie J├Ąger

Maintainer: Venu Thatikonda <thatikonda92 at>

Citation (from within R, enter citation("ALPS")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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biocViews ATACSeq, ChIPSeq, Epigenetics, HistoneModification, Sequencing, Software, Transcription, Visualization
Version 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports assertthat, BiocParallel, ChIPseeker, corrplot, data.table, dplyr, GenomicRanges, GGally, genefilter, gghalves, ggplot2, ggseqlogo, Gviz, magrittr,, plyr, reshape2, rtracklayer, stats, stringr, tibble, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, utils
Suggests knitr, rmarkdown, ComplexHeatmap, circlize, testthat
Depends On Me
Imports Me
Suggests Me
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Source Package ALPS_1.0.0.tar.gz
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Mac OS X 10.11 (El Capitan) ALPS_1.0.0.tgz
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