ChIC

This package is for version 3.12 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: 3.12

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 "4.0") 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 1.10.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-2
Depends spp, R (>= 3.6)
Imports ChIC.data(>= 1.7.1), 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_1.10.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) ChIC_1.10.0.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 3.12 Source Archive