ALPS

DOI: 10.18129/B9.bioc.ALPS    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ALPS.

AnaLysis routines for ePigenomicS data

Bioconductor version: Release (3.14)

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

BiocManager::install("ALPS")

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

Documentation

PDF		Reference Manual

Details

biocViews	ATACSeq, ChIPSeq, Epigenetics, HistoneModification, Sequencing, Software, Transcription, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.10 (R-3.6) (2.5 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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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