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- Reverse Engineering and Analysis of Regulatory Networks
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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