Browse by Software Type
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- Reverse Engineering and Analysis of Regulatory Networks
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- Integration of Genomics Data
- Immuno-Genomics Data Analysis
- Protein Interaction Prediction
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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 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