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

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

Scripts for analyzing T cell receptor repertoire sequencing data.

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

A tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.

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

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

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

A program to compare and align protein structures.

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

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

Programs that calculate solvent accessible surface area and curvature-corrected solvent accessible surface area.

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.

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

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

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

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