ChIC

DOI: 10.18129/B9.bioc.ChIC  

Quality Control Pipeline for ChIP-Seq Data

Bioconductor version: Release (3.16)

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>

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

Installation

To install this package, start R (version "4.2") 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 1.18.0
In Bioconductor since BioC 3.7 (R-3.5) (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
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ChIC_1.18.0.tar.gz
Windows Binary
macOS Binary (x86_64) ChIC_1.18.0.tgz
macOS Binary (arm64) ChIC_1.18.0.tgz
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: