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 <email@example.com>|
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