ChIC

DOI:10.18129/B9.bioc.ChIC

This is thedevelopmentversion of ChIC; for the stable release version, seeChIC.

Quality Control Pipeline for ChIP-Seq Data

Bioconductor version: Development (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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("ChIC")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("ChIC")

PDF	R Script	ChIC
PDF		Reference Manual

Details

biocViews	ChIPSeq,QualityControl,Software
Version	1.17.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 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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Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package	ChIC_1.17.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	ChIC_1.17.0.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	//www.anjoumacpherson.com/packages/ChIC/
Package Downloads Report	Download Stats