chroGPS

DOI: 10.18129/B9.bioc.chroGPS    

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 3.11 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: 3.11

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 "4.0") 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

PDF		Reference Manual

Details

biocViews	ChIPSeq, ChIPchip, Clustering, DataRepresentation, Epigenetics, HistoneModification, ImmunoOncology, Software, Visualization
Version	2.6.0
In Bioconductor since	BioC 2.11 (R-2.15) (8 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
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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/chroGPS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/chroGPS
Package Short Url	https://bioconductor.org/packages/chroGPS/
Package Downloads Report	Download Stats