ChIC

This package is for version 3.10 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: 3.10

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 (version "3.6") 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")
ChIC PDF R Script
Reference Manual PDF

Details

biocViews ChIPSeq, QualityControl, Software
Version 1.6.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-2
Depends spp, R (>= 3.6)
Imports ChIC.data(>= 1.3.3), caTools, methods, GenomicRanges, IRanges, parallel, progress, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics
System Requirements
URL
See More
Suggests
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package ChIC_1.6.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) ChIC_1.6.0.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
Old Source Packages for BioC 3.10 Source Archive