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

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Documentation for package ‘FunChIP’ version 1.28.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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FunChIP-package	Clustering and Alignment of ChIP-Seq peaks based on their shapes
bending_index	The elbow rule to define the proper number of clusters.
choose_k	Choice of the final classification of peaks
choose_k-method	Choice of the final classification of peaks
cluster_peak	Clustering the peaks with the k-mean alignment algorithm
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 among their derivatives.
FunChIP	Clustering and Alignment of ChIP-Seq peaks based on their shapes
GR	Peaks of a ChIP-seq experiment
GR100	Peaks of a ChIP-seq experiment
peaks	Coverage of a ChIP-Seq experiment
peaks.data	Coverage of a ChIP-Seq experiment
peaks.data.classified	Coverage of a ChIP-Seq experiment
peaks.data.classified.scaled	Coverage of a ChIP-Seq experiment
peaks.data.cluster	Coverage of a ChIP-Seq experiment
peaks.data.cluster.scaled	Coverage of a ChIP-Seq experiment
peaks.data.smooth	Coverage of a ChIP-Seq experiment
peaks.data.smooth.scaled	Coverage of a ChIP-Seq experiment
peaks.data.summit	Coverage of a ChIP-Seq experiment
peaks.data.summit.scaled	Coverage of a ChIP-Seq experiment
pileup_peak	Computing read counts on a GRanges object.
pileup_peak-method	Computing read counts on a GRanges object.
plot_peak	Plotting the peaks.
plot_peak-method	Plotting the peaks.
silhouette_plot	Return the silhouette index for clustered peaks
smooth_peak	Spline smoothing of the peak
smooth_peak-method	Spline smoothing of the peak
summit_peak	Finding the summits of the peaks of the GRanges object
summit_peak-method	Finding the summits of the peaks of the GRanges object