To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("csaw")
In most cases, you don't need to download the package archive at all.
csaw
ChIP-seq analysis with windows
Bioconductor version: 3.0
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Author: Aaron Lun <alun at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>
Maintainer: Aaron Lun <alun at wehi.edu.au>
Citation (from within R,
enter citation("csaw")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("csaw")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("csaw")
| R Script | csaw Vignette | |
| csawUserGuide.pdf | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, ChIPSeq, Coverage, Genetics, MultipleComparison, Normalization, Sequencing, Software |
| Version | 1.0.7 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL-3 |
| Depends | R (>= 3.1.0), GenomicRanges |
| Imports | Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, GenomicAlignments, S4Vectors, IRanges, GenomeInfoDb |
| LinkingTo | |
| Suggests | org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene |
| 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 | csaw_1.0.7.tar.gz |
| Windows Binary | csaw_1.0.7.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | csaw_1.0.7.tgz |
| Mac OS X 10.9 (Mavericks) | csaw_1.0.7.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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