ChIC

DOI: 10.18129/B9.bioc.ChIC    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ChIC.

Quality Control Pipeline for ChIP-Seq Data

Bioconductor version: 3.9

Quality control (QC) pipeline for ChIP-seq data using a comprehensive set of QC metrics, including previously proposed metrics as well as novel ones, based on local characteristics of the enrichment profile. The package provides functions to calculate a set of QC metrics, a compendium with reference values and machine learning models to score sample quality.

Author: Carmen Maria Livi

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChIC")

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("ChIC")

 

PDF	R Script	ChIC
PDF		Reference Manual

Details

biocViews	ChIPSeq, QualityControl, Software
Version	1.4.0
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
License	GPL-2
Depends	spp, R (>= 3.5)
Imports	ChIC.data(>= 1.3.3), caTools, methods, GenomicRanges, IRanges, parallel, progress, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics
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Package Archives

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

Source Package	ChIC_1.4.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	ChIC_1.4.0.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	https://bioconductor.org/packages/ChIC/
Package Downloads Report	Download Stats