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

Functions

choose_k Man page
choose_k,GRanges-method Man page
choose_k-method Man page
cluster_peak Man page
cluster_peak,GRanges-method Man page
cluster_peak-method Man page
compute_fragments_length Man page
distance_peak Man page
FunChIP Man page
FunChIP-package Man page
GR Man page
GR100 Man page
peaks Man page
peaks.data Man page
peaks.data.classified Man page
peaks.data.classified.scaled Man page
peaks.data.cluster Man page
peaks.data.cluster.scaled Man page
peaks.data.smooth Man page
peaks.data.smooth.scaled Man page
peaks.data.summit Man page
peaks.data.summit.scaled Man page
pileup_peak Man page
pileup_peak,GRanges-method Man page
pileup_peak-method Man page
plot_peak Man page
plot_peak,GRanges-method Man page
plot_peak-method Man page
smooth_peak Man page
smooth_peak,GRanges-method Man page
smooth_peak-method Man page
summit_peak Man page
summit_peak,GRanges-method Man page
summit_peak-method Man page

Files

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

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