FunChIP

DOI: 10.18129/B9.bioc.FunChIP    

Clustering and Alignment of ChIP-Seq peaks based on their shapes

Bioconductor version: Release (3.13)

Preprocessing and smoothing of ChIP-Seq peaks and efficient implementation of the k-mean alignment algorithm to classify them.

Author: Alice Parodi [aut, cre], Marco Morelli [aut, cre], Laura M. Sangalli [aut], Piercesare Secchi [aut], Simone Vantini [aut]

Maintainer: Alice Parodi <alicecarla.parodi at polimi.it>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FunChIP")

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("FunChIP")

 

PDF	R Script	An introduction to FunChIP
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, Clustering, Software, StatisticalMethod
Version	1.18.0
In Bioconductor since	BioC 3.4 (R-3.3) (5 years)
License	Artistic-2.0
Depends	R (>= 3.2), GenomicRanges
Imports	shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer
LinkingTo	Rcpp
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	FunChIP_1.18.0.tar.gz
Windows Binary	FunChIP_1.18.0.zip
macOS 10.13 (High Sierra)	FunChIP_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FunChIP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FunChIP
Package Short Url	https://bioconductor.org/packages/FunChIP/
Package Downloads Report	Download Stats