To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CexoR")
In most cases, you don't need to download the package archive at all.
CexoR
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Bioconductor version: 3.0
Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalized count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package 'idr'.
Author: Pedro Madrigal <pm12 at sanger.ac.uk>
Maintainer: Pedro Madrigal <pm12 at sanger.ac.uk>
Citation (from within R,
enter citation("CexoR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CexoR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CexoR")
| R Script | CexoR Vignette | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | Genetics, Sequencing, Software, Transcription |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | Artistic-2.0 | GPL-2 + file LICENSE |
| Depends | R (>= 2.10.0), S4Vectors, IRanges |
| Imports | Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, BiocStyle |
| SystemRequirements | |
| Enhances | |
| 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 | CexoR_1.4.0.tar.gz |
| Windows Binary | CexoR_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | CexoR_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | CexoR_1.4.0.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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