Software

rmspc: Multiple Sample Peak Calling

R/Bioconductor package that runs MSPC (Multiple Sample Peak Calling) software using R. MSPC uses combined evidence from ChIP-seq replicated experiments to evaluate peak calling output, rescuing peaks, and reduce false positives.
Software
Preprint

ProbKMA-FMD: Functional Motif Discovery via ProbKMA

R code implementing ProbKMA (probabilistic K-mean with local alignment) for local clustering of functional data and functional motif discovery.
Software
Publication

IWTomics: Interval-Wise Testing for Omics Data

R/Bioconductor package that implements the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in “Omics” data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.
Software
Software on Galaxy
Tutorial on Galaxy
Publication

SIC-ChIP: Shape Index Clustering for ChIP-seq peaks

Command line R script to cluster the peaks of a ChIP-seq experiment taking into consideration both their shape and their intensity.
Software
Publication