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

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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]
Date of publication
None
Maintainer
Alice Parodi <alicecarla.parodi@polimi.it>
License
Artistic-2.0
Version
1.0.0

View on Bioconductor

Man pages

choose_k-method
Choice of the final classification of peaks
cluster_peak-method
Clustering the peaks with the k-mean alignment algorithm
compute_fragments_length
Computing the length of the fragments in the .bam file.
distance_peak
Computing distance matrices among spline-smoothed peaks and...
FunChIP-package
Clustering and Alignment of ChIP-Seq peaks based on their...
GR100
Peaks of a ChIP-seq experiment
peaks
Coverage of a ChIP-Seq experiment
pileup_peak-method
Computing read counts on a GRanges object.
plot_peak-method
Plotting the peaks.
smooth_peak-method
Spline smoothing of the peak
summit_peak-method
Finding the summits of the peaks of the GRanges object

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