ALPS
This package is for version 3.10 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: 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 Jäger
Maintainer: Venu Thatikonda <thatikonda92 at gmail.com>
citation("ALPS")):
Installation
To install this package, start R (version "3.6") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ALPS")| ALPS-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, ChIPSeq, Epigenetics, HistoneModification, Sequencing, Software, Transcription, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 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 |
| System Requirements | |
| URL | https://github.com/itsvenu/ALPS |
| Bug Reports | https://github.com/itsvenu/ALPS/issues |
See More
| Suggests | knitr, rmarkdown, ComplexHeatmap, circlize, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ALPS/ |
| Package Short Url | https://bioconductor.org/packages/ALPS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |