ChIC

DOI: 10.18129/B9.bioc.ChIC    

Quality Control Pipeline for ChIP-Seq Data

Bioconductor version: Release (3.8)

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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ChIC", version = "3.8")

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 1.2.0
License GPL-2
Depends spp, R (>= 3.5)
Imports ChIC.data(>= 1.1.4), 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_1.2.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) ChIC_1.2.0.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/
Package Downloads Report Download Stats

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