FunChIP

DOI: 10.18129/B9.bioc.FunChIP    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see FunChIP.

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

Bioconductor version: 3.9

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 "3.6") 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	1.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 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
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SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	FunChIP_1.10.0.tar.gz
Windows Binary	FunChIP_1.10.0.zip
Mac OS X 10.11 (El Capitan)	FunChIP_1.10.0.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