ChIC

This package is for version 3.7 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: 3.7

Quality control pipeline for ChIP-seq data using a comprehensive set of quality control metrics, including previously proposed metrics as well as novel ones, based on local characteristics of the enrichment profile. The framework allows assessing quality of samples with sharp or broad enrichment profiles, whereas previously proposed metrics were not taking this into account. CHIC provides a reference compendium of quality control metrics and trained machine learning models for scoring samples.

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 "3.5") 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 1.0.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-2
Depends spp, R (>= 3.5)
Imports ChIC.data(>= 0.99), caTools, methods, GenomicRanges, IRanges, parallel, 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_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) ChIC_1.0.0.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 https://bioconductor.org/packages/ChIC/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive