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chipenrich.data
Gene set enrichment analysis for ChIP-seq data
Bioconductor version: 3.0
Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates.
Author: Ryan P. Welch [aut, cre, cph], Chee Lee [aut, cre], Raymond G. Cavalcante [aut, cre], Laura J. Scott [ths], Maureen A. Sartor [ths]
Maintainer: Ryan P. Welch <welchr at umich.edu>, Chee Lee <cheelee at umich.edu>, Raymond G. Cavalcante <rcavalca at umich.edu>
Citation (from within R,
enter citation("chipenrich.data")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("chipenrich.data")
Documentation
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ExperimentData |
| Version | 1.1.8 |
| License | GPL-3 |
| Depends | R (>= 2.15.0) |
| Imports | methods, GenomicRanges(>= 1.10.0), IRanges(>= 1.16.0), BiocGenerics(>= 0.2.0) |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | chipenrich |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | chipenrich.data_1.1.8.tar.gz |
| Windows Binary | chipenrich.data_1.1.8.zip |
| Mac OS X 10.6 (Snow Leopard) | chipenrich.data_1.1.8.tgz |
| Mac OS X 10.9 (Mavericks) | chipenrich.data_1.1.8.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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