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>

Citation (from within R, enter citation("FunChIP")):

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
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_1.10.0.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

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