FunChIP

DOI: 10.18129/B9.bioc.FunChIP    

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

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("FunChIP")

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	1.4.0
In Bioconductor since	BioC 3.4 (R-3.3) (1.5 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
Build Report

Package Archives

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

Source Package	FunChIP_1.4.0.tar.gz
Windows Binary	FunChIP_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	FunChIP_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FunChIP
Package Short Url	http://bioconductor.org/packages/FunChIP/
Package Downloads Report	Download Stats