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("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 | R Script | |
| Reference Manual |
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 |
| 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_1.0.0.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 |