ChIC

DOI: 10.18129/B9.bioc.ChIC  

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ChIC.

Quality Control Pipeline for ChIP-Seq Data

Bioconductor version: 3.17

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 external.ifom.eu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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	1.19.0
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 years)
License	GPL-2
Depends	spp, R (>= 3.6)
Imports	ChIC.data(>= 1.11.1), caTools, methods, GenomicRanges, IRanges, parallel, progress, randomForest, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics, genomeIntervals, Rsamtools
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Package Archives

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

Source Package	ChIC_1.19.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/ChIC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIC
Bioc Package Browser	https://code.bioconductor.org/browse/ChIC/
Package Short Url	https://bioconductor.org/packages/ChIC/
Package Downloads Report	Download Stats