ChIC

DOI: 10.18129/B9.bioc.ChIC    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see ChIC.

Quality Control Pipeline for ChIP-Seq Data

Bioconductor version: 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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/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 [email protected]:packages/ChIC
Package Short Url	http://bioconductor.org/packages/ChIC/
Package Downloads Report	Download Stats