Randomly
Lead Investigator(s) Raul Rabadan
Randomly is a python package for denoising single-cell data using Random Matrix Theory.
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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.
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Repertoire
Lead Investigator(s) Yufeng Shen
Scripts for analyzing T cell receptor repertoire sequencing data.
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SAVI
Lead Investigator(s) Raul Rabadan
A program for calling variants in high-throughput sequencing data, particularly paired tumor-normal samples.
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SCREEN
Lead Investigator(s) Barry Honig
A tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.
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scTDA
Lead Investigator(s) Raul Rabadan
An object-oriented python library for topological data analysis of high-throughput single-cell RNA-seq data.
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ShareViz
Lead Investigator(s) Itsik Pe'er
A tool for graphical visualization of hidden relatedness based on GERMLINE output.
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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.
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Ska
Lead Investigator(s) Barry Honig
A program to compare and align protein structures.
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SkyLine
Lead Investigator(s)
A high-throughput pipeline for homology modeling of protein structures.
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SPLASH
Lead Investigator(s) Andrea Califano
A deterministic pattern discovery algorithm that can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences.
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Splicescope
Lead Investigator(s) Chaolin Zhang
A method to evaluate neuronal maturation based on alternative splicing profiles.
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STING Millennium
Lead Investigator(s) Barry Honig
A web-based suite of programs for the comprehensive and simultaneous analysis of structure and sequence.
SURFace
Lead Investigator(s) Barry Honig
Programs that calculate solvent accessible surface area and curvature-corrected solvent accessible surface area.
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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.
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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.
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Target Explorer
Lead Investigator(s) Barry Honig, Richard Mann
Automates the process of predicting the complex regulatory elements for a specified set of transcription factors in the Drosophila melanogaster genome.
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TEISER
Lead Investigator(s) Saeed Tavazoie
A de-novo motif discovery tool for finding informative structural elements in RNA.
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TOBI
Lead Investigator(s) Raul Rabadan
TOBI predicts somatic variants from .vcf or .bam input.
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TranscriptionDetector
Lead Investigator(s) Harmen Bussemaker
A tool for finding probes that measures significantly expressed loci in a genomic array experiment.
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