chroGPS
This package is for version 3.9 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: 3.9
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("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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, ChIPchip, Clustering, DataRepresentation, Epigenetics, HistoneModification, ImmunoOncology, Software, Visualization |
| Version | 2.2.0 |
| 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 |
See More
| 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_2.2.0.tar.gz |
| Windows Binary | chroGPS_2.2.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | chroGPS_2.2.0.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 3.9 | Source Archive |