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
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
Biolearn 1.0
Lead Investigator(s) Dana Pe'er
A package for applying probabilistic graphical models to biological applications.
Software Page
Camelot
Lead Investigator(s) Dana Pe'er
CAusal Modeling with Expression Linkage for cOmplex Traits (Camelot) provides a framework to both model complex traits and identify the potential underlying causal factors.
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
CIMS
Lead Investigator(s) Chaolin Zhang
A computational method for HITS-CLIP data analysis to determine the exact protein-RNA crosslink sites and thereby map protein-RNA interactions at single-nucleotide resolution.
Software Page
CLEANER
Lead Investigator(s) Mariano Alvarez
An R-system software package for the assembly of informative, transcript-specific probe-clusters for Affymetrix expression microarrays.
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
CONEXIC
Lead Investigator(s) Dana Pe'er
COpy Number and EXpression In Cancer (CONEXIC) is an algorithm that integrates matched copy number (amplifications and deletions) and gene expression data from tumor samples to identify driving mutations and the processes they influence.
Software Page
cryoEM Refinement Tools
Lead Investigator(s) Barry Honig
Programs and protocols for refining atomic structures — either experimentally determined or computationally constructed — within cryo-electron microscopy (cryoEM) density maps of macromolecular complexes.
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
DREVI and DREMI
Lead Investigator(s) Dana Pe'er
Algorithms for visualizing and scoring the strengths of pairwise interactions in single-cell data.
Software Page
EDGI
Lead Investigator(s) Barry Honig
EDGI (Enhancer Detection using only Genomic Information) identifies large regulatory elements that consist of evolutionarily conserved, order-independent clusters of short conserved motifs.
Software Page
Energy Functions
Lead Investigator(s) Barry Honig
Programs for evaluating or comparing protein structure predictions.
Software Page
EVE
Lead Investigator(s) Saeed Tavazoie
A simulation framework for microbial populations in complex dynamic environments.
Software Page