csawUsersGuide
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see csawUsersGuide.
csaw User's Guide
Bioconductor version: 3.9
A user's guide for the csaw package for detecting differentially bound regions in ChIP-seq data. Describes how to read in BAM files to obtain a per-window count matrix, filtering to obtain high-abundance windows of interest, normalization of sample-specific biases, testing for differential binding, consolidation of per-window results to obtain per-region statistics, and annotation and visualization of the DB results.
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("csawUsersGuide")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("csawUsersGuide")
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("csawUsersGuide")| User's guide | R Script |
Details
| biocViews | EpigeneticsWorkflow, Workflow |
| Version | 1.0.0 |
| License | GPL-3 |
| Depends | |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | csaw, chipseqDBData, edgeR, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, rtracklayer, Rsamtools, Gviz, knitr, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | csawUsersGuide_1.0.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| Source Repository | git clone https://git.bioconductor.org/packages/csawUsersGuide |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/csawUsersGuide |
| Package Short Url | https://bioconductor.org/packages/csawUsersGuide/ |
| Package Downloads Report | Download Stats |