FunChIP: Clustering and Alignment of ChIP-Seq peaks based on their shapes
Version 1.2.0

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]
Bioconductor views ChIPSeq Clustering StatisticalMethod
Date of publicationNone
MaintainerAlice Parodi <alicecarla.parodi@polimi.it>
LicenseArtistic-2.0
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FunChIP")

Getting started

Package overview

Popular man pages

bending_index: The elbow rule to define the proper number of clusters.
choose_k-method: Choice of the final classification of peaks
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
silhouette_plot: Return the silhouette index for clustered peaks
summit_peak-method: Finding the summits of the peaks of the GRanges object
See all...

All man pages Function index File listing

Man pages

bending_index: The elbow rule to define the proper number of clusters.
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.
silhouette_plot: Return the silhouette index for clustered peaks
smooth_peak-method: Spline smoothing of the peak
summit_peak-method: Finding the summits of the peaks of the GRanges object

Functions

FunChIP Man page
FunChIP-package Man page
GR Man page
GR100 Man page
bending_index Man page Source code
choice_lambda_spline Source code
choose.k.GRange Source code
choose_d Source code
choose_k Man page
choose_k,GRanges-method Man page
choose_k-method Man page
cluster.GRange Source code
cluster_peak Man page
cluster_peak,GRanges-method Man page
cluster_peak-method Man page
compute_average_distance Source code
compute_distance Source code
compute_distance_with_shift Source code
compute_fragments_length Man page Source code
compute_silhouette Source code
convert_vectors_to_list Source code Source code
define_new_grid Source code
definition_spline Source code
distance_peak Man page Source code
distance_point_line Source code
extension Source code
extension_with_min Source code
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.GRange Source code
pileup_peak Man page
pileup_peak,GRanges-method Man page
pileup_peak-method Man page
plot.GRange Source code
plot_peak Man page
plot_peak,GRanges-method Man page
plot_peak-method Man page
plot_row_data Source code
silhouette_plot Man page Source code
smooth.GRange Source code
smooth_peak Man page
smooth_peak,GRanges-method Man page
smooth_peak-method Man page
summit.GRange Source code
summit_peak Man page
summit_peak,GRanges-method Man page
summit_peak-method Man page
unlist.counts Source code Source code Source code Source code

Files

DESCRIPTION
NAMESPACE
R
R/bending_index.R
R/choose.k.GRange.R
R/cluster.GRange.R
R/compute.d.GRange.R
R/distance.GRange.R
R/pileup.peak.GRange.R
R/plot.GRange.R
R/silhouette_plot.R
R/smooth.GRange.R
R/summit.GRange.R
build
build/vignette.rds
data
data/GR100.rda
data/peaks.rda
inst
inst/NEWS
inst/doc
inst/doc/FunChIP.R
inst/doc/FunChIP.Rnw
inst/doc/FunChIP.pdf
inst/extdata
inst/extdata/test.bam
inst/extdata/test.bam.bai
man
man/FunChIP-package.Rd
man/GR100.Rd
man/bending_index.Rd
man/choose_k-method.Rd
man/cluster_peak-method.Rd
man/compute_fragments_length.Rd
man/distance_peak.Rd
man/peaks.Rd
man/pileup_peak-method.Rd
man/plot_peak-method.Rd
man/silhouette_plot.Rd
man/smooth_peak-method.Rd
man/summit_peak-method.Rd
src
src/Makevars
src/Makevars.win
src/kmean_function.cpp
src/peak.h
vignettes
vignettes/FunChIP.Rnw
vignettes/mybib.bib
FunChIP documentation built on May 20, 2017, 10:43 p.m.

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