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

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

AuthorAlice Parodi [aut, cre], Marco Morelli [aut, cre], Laura M. Sangalli [aut], Piercesare Secchi [aut], Simone Vantini [aut]
Date of publicationNone
MaintainerAlice Parodi <alicecarla.parodi@polimi.it>
LicenseArtistic-2.0
Version1.0.0

View on Bioconductor

Files in this package

FunChIP/DESCRIPTION
FunChIP/NAMESPACE
FunChIP/R
FunChIP/R/choose.k.GRange.R FunChIP/R/cluster.GRange.R FunChIP/R/compute.d.GRange.R FunChIP/R/distance.GRange.R FunChIP/R/pileup.peak.GRange.R FunChIP/R/plot.GRange.R FunChIP/R/smooth.GRange.R FunChIP/R/summit.GRange.R
FunChIP/build
FunChIP/build/vignette.rds
FunChIP/data
FunChIP/data/GR100.rda
FunChIP/data/peaks.rda
FunChIP/inst
FunChIP/inst/NEWS
FunChIP/inst/doc
FunChIP/inst/doc/FunChIP.R
FunChIP/inst/doc/FunChIP.Rnw
FunChIP/inst/doc/FunChIP.pdf
FunChIP/inst/extdata
FunChIP/inst/extdata/test.bam
FunChIP/inst/extdata/test.bam.bai
FunChIP/man
FunChIP/man/FunChIP-package.Rd FunChIP/man/GR100.Rd FunChIP/man/choose_k-method.Rd FunChIP/man/cluster_peak-method.Rd FunChIP/man/compute_fragments_length.Rd FunChIP/man/distance_peak.Rd FunChIP/man/peaks.Rd FunChIP/man/pileup_peak-method.Rd FunChIP/man/plot_peak-method.Rd FunChIP/man/smooth_peak-method.Rd FunChIP/man/summit_peak-method.Rd
FunChIP/src
FunChIP/src/Makevars
FunChIP/src/Makevars.win
FunChIP/src/kmean_function.cpp
FunChIP/src/peak.h
FunChIP/vignettes
FunChIP/vignettes/FunChIP.Rnw
FunChIP/vignettes/mybib.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.