ALPS

DOI: 10.18129/B9.bioc.ALPS    

AnaLysis routines for ePigenomicS data

Bioconductor version: Release (3.13)

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 Jäger

Maintainer: Venu Thatikonda <thatikonda92 at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ALPS")

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

Documentation

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

browseVignettes("ALPS")

 

HTML	R Script	ALPS-vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ATACSeq, ChIPSeq, Epigenetics, HistoneModification, Sequencing, Software, Transcription, Visualization
Version	1.5.0
In Bioconductor since	BioC 3.10 (R-3.6) (2 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	assertthat, BiocParallel, ChIPseeker, corrplot, data.table, dplyr, GenomicRanges, GGally, genefilter, gghalves, ggplot2, ggseqlogo, Gviz, magrittr, org.Hs.eg.db, plyr, reshape2, rtracklayer, stats, stringr, tibble, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, utils
LinkingTo
Suggests	knitr, rmarkdown, ComplexHeatmap, circlize, testthat
SystemRequirements
Enhances
URL	https://github.com/itsvenu/ALPS
BugReports	https://github.com/itsvenu/ALPS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ALPS_1.5.0.tar.gz
Windows Binary	ALPS_1.5.0.zip
macOS 10.13 (High Sierra)	ALPS_1.5.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ALPS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ALPS
Package Short Url	https://bioconductor.org/packages/ALPS/
Package Downloads Report	Download Stats