Software tools and Projects

Integrating gene expression and DNA methylation datasets for disjoint sample sets.

Selecting minimizers based on minimum decycling set.

MDS Minimizers
MDS Minimizers homepage

Long-read mapping using syncmers.

Syncmer Mapping
Syncmer Mapping homepage

CT-FOCS - A database of cell type-specific enhancer-promoter links

Dataset adaptive minimizer order generator for binning applications

AdaOrder and DGerbil
AdaOrder and DGerbil homepage

3-class classification of metagenome assemblies

Accurate module discovery using gene activities and a network

Multi Omic clustering by Non-Exhaustive Types

Complete plasmid assembly in metagenomes

Empirically correcting the functional significance of GO terms in modules

PlasClass - Plasmid sequence classifier

PlasClass homepage

NEMO: Neighborhood based multi-omics clustering algorithm

PROMO - a tool for analysis and visualization of large multi-omic and clinical datasets.

EXPANDER - A one stop-shop platform for all analysis steps of gene expression data.

Faucet: streaming de novo assembly graph construction

FOCS: A database of human and mouse enhancer-promoter links

Adeptus - A database and tools for multi-disease analysis.

Recycler - detecting plasmids from de novo assembly graphs

DOCKS - A software for designing  compact universal k-mers hitting set.

RichMind - Analysis of enrichment within neuroimaging findings

ElemeNT - Tool for detection of core promoter elements.

TWIGS - Three-Way module Inference via Gibbs Sampling.

Motif finding from high-throughput SELEX

ModMap - Detecting maps of modules by simultaneous analysis of two biological networks.

BARCODE - A fast lossless read compression tool based on Bloom filters.

ShortCAKE - Designing a shortest DNA sequence that covers all k-mers, exploiting reverse complementarity.

ShortCake homepage

Dicer - A tool for advanced analysis of differential co-expression (DC) case-control gene expression data

RAP - A software for inferring binding site motifs from protein binding microarrays.

HiDe - A software for inferring highways of horizontal gene transfer.

Morph - A webtool and software for ranking candidate genes in pathways.

ALLEGRO - Software for simultaneous discovery of cis-regulatory motifs and their associated expression profiles.

AMADEUS - Platform for de novo motif discovery in DNA sequences.

ModEnt - A tool that reconstructs gene regulatory networks from high throughput experimental data.

STACK - Analyzing statistical associations among cancer karyotypes.

FAME - A tool for Functional Assignment to MicroRNAs via Enrichment

TORQUE - Topology-free querying of protein interaction networks.

SPIKE - (previously SHARP). Signaling pathways integrated knowledge engine.

HYDEN - A software for designing degenerate primers.

MetaReg - A tool for modeling of biological systems

GEVALT - An integrated software for genotype analysis.

PSAT - Evaluating the significance of association scores in whole-genome cohorts with stratification.

Cofactors - Linking transcription factors and chromatin modifiers.

cofactors homepage

MATISSE - A tool for joint analysis of interaction networks and gene expression data.

RAT - A software for rapid association tests.

Cisprof - Evolutionary mechanisms underlying conservation and evolvability in regulatory networks.

SIMBA -  System level analysis of yeast by exploring of large-scale biological compendia.

PREVO - An analysis of the network of selection forces in the evolution of yeast cis-regulation

SAMBA - Module discovery in highly diverse genome-wide datasets using biclustering.

GREAL - software for the graph realization Problem.

PRIMA - A program for finding transcription factors whose binding sites are enriched in a given set of promoters.

PIVOT - Java-based protein interactions visualization tool.

The following software tools were phased out. Individuals wishing to use any of them should contact Ron Shamir.

Pmemap (Nat Struc Mol Bio 2011)
ReL (PLoS Genetics 2010)
Cezanne (Bioinformatics 2009)
Degas (PLoS One 2010)