chroGPS

DOI: 10.18129/B9.bioc.chroGPS    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see chroGPS.

chroGPS2: Generation, visualization and differential analysis of epigenome maps

Bioconductor version: 3.8

We provide intuitive maps to visualize, analyze and compare the association between genetic elements based on their epigenetic profiles. The approach is based on Multi-Dimensional Scaling, and includes a parallelized implementation for handling high dimensional datasets. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds. We also provide functions and methods to perform differential analysis of epigenome maps at factor and gene level.

Author: Oscar Reina, David Rossell

Maintainer: Oscar Reina <oscar.reina at irbbarcelona.org>

Installation

To install this package, start R (version "3.5") and enter:

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

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("chroGPS")

 

PDF	R Script	Manual for the chroGPS library
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, ChIPchip, Clustering, DataRepresentation, Epigenetics, HistoneModification, ImmunoOncology, Software, Visualization
Version	2.0.1
In Bioconductor since	BioC 2.11 (R-2.15) (6.5 years)
License	GPL (>=2.14)
Depends	R (>= 3.2.0), GenomicRanges, IRanges, methods, Biobase, MASS, graphics, stats, changepoint
Imports	cluster, DPpackage, ICSNP, ellipse, vegan
LinkingTo
Suggests
SystemRequirements
Enhances	parallel, XML, rgl, gplots, pheatmap, ChIPpeakAnno, org.Dm.eg.db, caTools, plotly
URL
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	chroGPS_2.0.1.tar.gz
Windows Binary	chroGPS_2.0.1.zip
Mac OS X 10.11 (El Capitan)	chroGPS_2.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/chroGPS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/chroGPS
Package Short Url	http://bioconductor.org/packages/chroGPS/
Package Downloads Report	Download Stats