chroGPS

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 chroGPS.

chroGPS2: Generation, visualization and differential analysis of epigenome maps

Bioconductor version: 3.10

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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, ChIPchip, Clustering, DataRepresentation, Epigenetics, HistoneModification, ImmunoOncology, Software, Visualization
Version	2.4.0
In Bioconductor since	BioC 2.11 (R-2.15) (11.5 years)
License	GPL (>=2.14)
Depends	R (>= 3.2.0), GenomicRanges, IRanges, methods, Biobase, MASS, graphics, stats, changepoint
Imports	cluster, DPpackage, ICSNP, ellipse, vegan
System Requirements
URL

Suggests
Linking To
Enhances	parallel, XML, rgl, gplots, pheatmap, ChIPpeakAnno, org.Dm.eg.db, caTools, plotly
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	chroGPS_2.4.0.tar.gz
Windows Binary	chroGPS_2.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	chroGPS_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/chroGPS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/chroGPS
Bioc Package Browser	https://code.bioconductor.org/browse/chroGPS/
Package Short Url	https://bioconductor.org/packages/chroGPS/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.10	Source Archive