Software | Romualdi Lab

Samurai

A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).

gINTomics

An R package for Multi-Omics data integration and visualization

parmigine

Parallel Mutual Information Estimation for Gene Network Reconstruction

BrewerIX

Allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes

CliPPER

An R package for the identification of significant signal paths within significantly altered biological pathways.

graphite

graphite (GRAPH Interaction from pathway Topological Environment) is a computational framework to store, parse and convert pathway topologies to gene-gene networks.

microGraphite

An R pipeline to perform topological pathway analysis integrating gene and miRNA expression profiles

MOSCLIP

R package for multi-omic topological pathway analysis looking for survival-associated gene modules

PsiNorm

A scalable normalization for single-cell RNA-seq data

SimPATHy

a new method for simulating data from perturbed biological PATHways

SourceSet

A Graphical Model Approach to Identify Primary Genes in Perturbed Biological Pathways

topologyGSA

Gene Set Analysis Exploiting Pathway Topology