funMoDisco: Motif Discovery in Functional Data
R package implementing two complementary methodologies for discovering motifs in functional data: ProbKMA (probabilistic K-mean with local alignment) and FunBIalign. Both algorithms are suitable for single curves or sets of curves. The package also includes a flexible function to simulate functional data with embedded motifs, allowing users to generate benchmark datasets for validating and comparing motif discovery methods.
Software
ProbKMA publication
funBIalign publication
funInterMethSNP: Detecting SNP–Methylation Interaction Effects on Phenotypes
R package providing a functional regression framework to detect interaction effects between SNP genotypes (coded as 0/1/2) and DNA methylation profiles across various phenotypes. A key feature is the reconstruction of DNA methylation data as functional variables. The package implements models for continuous, binary, and count outcomes, and includes tools to reconstruct methylation curves and perform global hypothesis testing.
Software
Publication
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
Publication
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
Marzia A. Cremona 