ALPS

DOI: 10.18129/B9.bioc.ALPS    

AnaLysis routines for ePigenomicS data

Bioconductor version: Release (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 gmail.com>

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

Installation

To install this package, start R (version "3.6") 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 1.0.0
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, 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_1.0.0.tar.gz
Windows Binary ALPS_1.0.0.zip
Mac OS X 10.11 (El Capitan) ALPS_1.0.0.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

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