ChIC

DOI: 10.18129/B9.bioc.ChIC    

Quality Control Pipeline for ChIP-Seq Data

Bioconductor version: Release (3.7)

Quality control pipeline for ChIP-seq data using a comprehensive set of quality control metrics, including previously proposed metrics as well as novel ones, based on local characteristics of the enrichment profile. The framework allows assessing quality of samples with sharp or broad enrichment profiles, whereas previously proposed metrics were not taking this into account. CHIC provides a reference compendium of quality control metrics and trained machine learning models for scoring samples.

Author: Carmen Maria Livi

Maintainer: Carmen Maria Livi <carmen.livi at ifom.eu>

Citation (from within R, enter citation("ChIC")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ChIC")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChIC")

 

PDF R Script ChIC
PDF   Reference Manual

Details

biocViews ChIPSeq, QualityControl, Software
Version 1.0.0
License GPL-2
Depends spp, R (>= 3.5)
Imports ChIC.data(>= 0.99), caTools, methods, GenomicRanges, IRanges, parallel, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ChIC_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) ChIC_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChIC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChIC
Package Short Url http://bioconductor.org/packages/ChIC/
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