chroGPS

DOI: 10.18129/B9.bioc.chroGPS    

This is the development version of chroGPS; for the stable release version, see chroGPS.

chroGPS2: Generation, visualization and differential analysis of epigenome maps

Bioconductor version: Development (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>

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

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.5.0
In Bioconductor since BioC 2.11 (R-2.15) (7 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
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
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/
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