ChIC
This package is for version 3.16 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: 3.16
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 <carmen.livi at external.ifom.eu>
citation("ChIC")):
Installation
To install this package, start R (version "4.2") 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 | 1.18.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 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 |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIC_1.18.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | ChIC_1.18.0.tgz |
| macOS Binary (arm64) | ChIC_1.18.0.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 3.16 | Source Archive |