3DNA
Lead Investigator(s)Xiang-Jun Lu, Harmen Bussemaker

3DNA is a versatile, integrated software system for the analysis, rebuilding, and visualization of 3D nucleic-acid-containing structures. The 3DNA suite contains DSSR, an integrated software tool for dissecting the spatial structure of RNA, and SNAP for analyzing structures of nucleic acid-protein complexes.

Software Page
ADOMETA
Lead Investigator(s)Dennis Vitkup

A bioinformatics resource designed to predict genes for orphan metabolic activities — known biochemical activities not currently assigned to genes in some or all organisms.

Software Page
ARACNE
Lead Investigator(s)Andrea Califano

An algorithm for inferring gene regulatory networks from a set of microarray experiments.

Software Page
Atlas-SNP
Lead Investigator(s)Yufeng Shen

Bioinformatics analysis of next-generation sequencing.

Software Page
B Cell Interactome
Lead Investigator(s)Andrea Califano

A network of protein-protein, protein-DNA, and modulatory interactions in human B cells.

Software Page
Bias Removal
Lead Investigator(s)Andrea Califano

Two R scripts for removing location biases from a multiwell dataset.

Software Page
CANOES
Lead Investigator(s)Yufeng Shen

A method for calling copy number variants from exome sequencing data with an arbitrary number of reference samples.

Software Page
CONDEX (condr)
Lead Investigator(s)Itsik Pe'er

A hidden Markov model for detecting copy number variants in exome sequence data.

Software Page
CTK
Lead Investigator(s)Chaolin Zhang

A software package for comprehensive and streamlined analysis of CLIP data, including peak calling and identification of precise protein-RNA crosslink sites.

Software Page
DASH
Lead Investigator(s)Itsik Pe'er

DASH (DASH Associates Shared Haplotypes) is a tool for detecting association to clusters of identity by descent (IBD) segments detected by the Germline software tool.

Software Page
DelPhi
Lead Investigator(s)Barry Honig

Provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution.

Software Page
DeMAND
Lead Investigator(s)Andrea Califano

An efficient and accurate method for determining a drug's mechanism of action, including both direct drug targets and other gene products involved in implementing its effect or modulating its activity.

Software Page
DIGGIT
Lead Investigator(s)Andrea Califano

A Bioconductor package for identifying genetic variants that lie upstream of master regulators and drive cellular phenotypes.

Software Page
Episcore
Lead Investigator(s)Yufeng Shen

A method to predict gene haploinsufficiency based on human epigenomic profiles under normal conditions.

Software Page
EVE
Lead Investigator(s)Saeed Tavazoie

A simulation framework for microbial populations in complex dynamic environments.

Software Page
FASD
Lead Investigator(s)Raul Rabadan

Frequency Analysis of Sequence Data (FASD)

Software Page
FeatureREDUCE
Lead Investigator(s)Harmen Bussemaker

Software for inferring feature-based protein-DNA interaction models from protein binding microarray (PBM) data; used in Cis-BP database.

Software Page
FIRE
Lead Investigator(s)Saeed Tavazoie

A motif discovery and characterization program based on mutual information.

Software Page
FIRE-pro
Lead Investigator(s)Saeed Tavazoie

A motif discovery and characterization program for proteins based on mutual information.

Software Page
GAMToC
Lead Investigator(s)Raul Rabadan

Uses copy number and mutation data from a cohort of patients, for example from TCGA, to find modules of genes with a related mutation pattern.

Software Page
Germline
Lead Investigator(s)Itsik Pe'er

An algorithm for discovering long shared segments of identity by descent (IBD) between pairs of (unrelated) individuals in a large population.

Software Page
geWorkbench
Lead Investigator(s)Aris Floratos

Provides an integrated suite of genomics tools.

Software Page
HADiT
Lead Investigator(s)Itsik Pe'er

HADiT (Haplotype Amplification Distortion in Tumors) is a tool for computing and visualizing allelic distortion in tumor SNP data.

Software Page
HATS
Lead Investigator(s)Itsik Pe'er

A tool for calling amplified alleles and constructing the amplified haplotype within called tumor amplicons.

HERMES
Lead Investigator(s)Andrea Califano

Predicts competing endogenous RNA (ceRNA) interactions from expression profiles of candidate RNAs and their common miRNA regulators using conditional mutual information.

Software Page
HLA-IBD
Lead Investigator(s)Itsik Pe'er

A method for inferring per-locus human leukocyte antigen types using shared segments that are identical by descent (IBD), inferred from genotype data.

Software Page
HotSpots
Lead Investigator(s)Yufeng Shen

A method to infer cancer somatic mutation hotspots.

Software Page
Inference of Modules Associated with eQTL's
Lead Investigator(s)Itsik Pe'er

A tool for constructing modules regulated by eQTLs using gene expression and SNP variation data across multiple individuals.

INFOSTIP
Lead Investigator(s)Itsik Pe'er

A tool for selecting individual for sequencing by total information potential, based on GERMLINE output.

Software Page
iPAGE
Lead Investigator(s)Saeed Tavazoie

A functional and categorical enrichment program based on mutual information.

Software Page
JACKAL
Lead Investigator(s)Barry Honig
A collection of programs for the modeling and analysis of protein structures.
Software Page
LogoGenerator
Lead Investigator(s)Harmen Bussemaker

Generates “energy logos” representing the DNA binding specificity of transcription factors in a biophysically interpretable manner (letter height equals ddG/RT).

Software Page
MADSS
Lead Investigator(s)Nicholas Tatonetti

Network analysis framework that identifies adverse event (AE) neighborhoods within the human interactome (protein-protein interaction network).

Software Page
MARINa
Lead Investigator(s)Andrea Califano

The Master Regulator Inference Algorithm identifies transcription factors (TFs) that control the transition between the two phenotypes, A and B, and the maintenance of the latter phenotype.

Software Page
MatrixREDUCE
Lead Investigator(s)Harmen Bussemaker

Arguably the first “deep learning” model for fitting position-specific affinity matrix (PSAM) models to (continuously distributed) functional genomics data.

Software Page
mCarts
Lead Investigator(s)Chaolin Zhang

A hidden Markov model (HMM)-based method for predicting clusters of RNA motif sites.

Software Page
MINDy2/CINDY
Lead Investigator(s)Andrea Califano

An algorithm for the genome-wide discovery of modulators of transcriptional interactions.

Software Page
MODEST
Lead Investigator(s)Harris Wang

Developed with Morten Sommer, MODEST allows the rapid and effective design of optimal oligos for achieving specific mutations using the MAGE genome engineering platform.

Software Page
mRIN
Lead Investigator(s)Chaolin Zhang

A method for assessing a quantitative measure of mRNA integrity directly from RNA-seq data.

Software Page
MutaGeneSys
Lead Investigator(s)Itsik Pe'er

Uses genome-wide genotype data to estimate individual disease susceptibility.

Software Page
MVP
Lead Investigator(s)Yufeng Shen

Method to predict deleterious genetic effect of missense variants.

Software Page
Nest
Lead Investigator(s)Barry Honig
An algorithm for modeling protein structure based on a sequence-template alignment.
Software Page
NORI
Lead Investigator(s)Raul Rabadan

NORI (Non-coding RNA Identification) is a computational tool that identifies lncRNAs using next generation sequencing.

Software Page
OLego
Lead Investigator(s)Chaolin Zhang

A program for mapping RNA-seq reads, including de novo identification of exon junctions.

Software Page
OPERA
Lead Investigator(s)Itsik Pe'er

A tool for power estimation and design of whole-genome resequencing projects aimed at rare variant associations.

Software Page
P-HIPSTer
Lead Investigator(s)Barry Honig, Sagi Shapira
P-HIPSTer (Pathogen-Host Interactome Prediction using STructurE similaRity) is an algorithm that exploits both sequence- and structure-based information to infer interactions between pathogen and human proteins.
Software Page
Pandora
Lead Investigator(s)Raul Rabadan

A multi-step pipeline for finding pathogen sequences in RNA-seq data.

Software Page
Pegasus
Lead Investigator(s)Raul Rabadan

Enables annotation and prediction of oncogenic gene fusions using RNA-seq data.

Software Page
PoolDesign
Lead Investigator(s)Itsik Pe'er

A tool for designing overlapping pools for variant-carrier identification.

Software Page
PredUs
Lead Investigator(s)Barry Honig
A tool for the prediction of protein-protein interfaces based on interface conservation among structurally similar protein neighbors.
Software Page
PrePPI
Lead Investigator(s)Barry Honig
A database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
Software Page
Quantas
Lead Investigator(s)Chaolin Zhang

A pipeline for analyzing alternative splicing using RNA-seq data.

Software Page
Randomly
Lead Investigator(s)Raul Rabadan

Randomly is a python package for denoising single-cell data using Random Matrix Theory.

Software Page
REDUCE Suite
Lead Investigator(s)Harmen Bussemaker

A set of software tools for modeling the regulation of gene expression by transcription factors (TF); includes MatrixREDUCE, LogoGenerator, and Transfactivity.

Software Page
Repertoire
Lead Investigator(s)Yufeng Shen

Scripts for analyzing T cell receptor repertoire sequencing data.

Software Page
SAVI
Lead Investigator(s)Raul Rabadan

A program for calling variants in high-throughput sequencing data, particularly paired tumor-normal samples.

Software Page
SCREEN
Lead Investigator(s)Barry Honig
A tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.
Software Page
scTDA
Lead Investigator(s)Raul Rabadan

An object-oriented python library for topological data analysis of high-throughput single-cell RNA-seq data.

Software Page
ShareViz
Lead Investigator(s)Itsik Pe'er

A tool for graphical visualization of hidden relatedness based on GERMLINE output.

Software Page
SIXPAC
Lead Investigator(s)Itsik Pe'er

An efficient, scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets.

Software Page
Ska
Lead Investigator(s)Barry Honig

A program to compare and align protein structures.

Software Page
SkyLine
Lead Investigator(s)

A high-throughput pipeline for homology modeling of protein structures.

Software Page
Splicescope
Lead Investigator(s)Chaolin Zhang

A method to evaluate neuronal maturation based on alternative splicing profiles.

Software Page
SURFace
Lead Investigator(s)Barry Honig
Programs that calculate solvent accessible surface area and curvature-corrected solvent accessible surface area.
Software Page
T-profiler
Lead Investigator(s)Harmen Bussemaker

A web-based tool that uses the t-test to interpret genome-wide mRNA expression changes at the level of Gene Ontology categories or ChIP-based regulons.

Software Page
TARGet
Lead Investigator(s)Raul Rabadan

A light-weight application for reconstructing non-vertical evolutionary histories from sampled genetic sequences using persistent homology, a tool from topological data analysis.

Software Page
TEISER
Lead Investigator(s)Saeed Tavazoie

A de-novo motif discovery tool for finding informative structural elements in RNA.

Software Page
TOBI
Lead Investigator(s)Raul Rabadan

TOBI predicts somatic variants from .vcf or .bam input.

Software Page
TranscriptionDetector
Lead Investigator(s)Harmen Bussemaker

A tool for finding probes that measures significantly expressed loci in a genomic array experiment.

Software Page
VIPER
Lead Investigator(s)Andrea Califano

R-system package including the Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER) and the MAster Regulator INference Analysis (MARINA) algorithms.

Software Page
Xplorigin
Lead Investigator(s)Itsik Pe'er

A tool for parsing population ancestry of admixed individuals.

Software Page
Zinfandel
Lead Investigator(s)Itsik Pe'er, Yufeng Shen

A tool for detecting copy number variants (CNVs) whole genome data based on both depth of coverage and mate pair information.

Software Page