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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("chroGPS")
In most cases, you don't need to download the package archive at all.
chroGPS
chroGPS: visualizing the epigenome
Bioconductor version: 3.0
We provide intuitive maps to visualize the association between genetic elements, with emphasis on epigenetics. The approach is based on Multi-Dimensional Scaling. 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.
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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("chroGPS")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("chroGPS")
| R Script | Manual for the chroGPS library | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, Software, Visualization |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | GPL (>=2.14) |
| Depends | R (>= 2.13.0), IRanges, methods, Biobase, MASS, graphics, stats, changepoint |
| Imports | graphics, cluster, DPpackage, ICSNP |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | parallel, XML, rgl |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | chroGPS_1.10.0.tar.gz |
| Windows Binary | chroGPS_1.10.0.zip |
| Mac OS X 10.6 (Snow Leopard) | chroGPS_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | chroGPS_1.10.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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