Software

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arcasHLA is a tool for in silico inference of HLA genotypes (MHC class 1 and class 2) from RNA-seq.

Randomly is a python package for denoising single cell data with random matrix theory.

cancerdrugexplorer.org is a web app released with this publication to explore a set of cancer genomes collected and analyzed by Samsung Medical Center and The Rabadan Lab.

mutcomfocal is a tool for identifying recurrent and focal genomic alterations in tumor samples described in this publication.

Pandora is a tool for the identification and discovery of tumor-associated microbes via RNAseq.

Pancancer is a web app to explore genetic alterations in TCGA (The Cancer Genome Atlas) using Topological Data Analysis.

Primate Marburg Infection Gene Expression Explorer is a web app for exploring the gene expression of primates infected with Marburg virus.

Pegasus is a tool for the annotation and prediction of oncogenic gene fusions in RNAseq.

GAMToC 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.

Genome Browser is the Rabadan Lab's locally hosted implementation of the UCSC Genome Browser. Currently, it features the mm9 exotome and various annotated non-human primate assemblies.

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

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

Motor Neurons scTDA is a GUI to browse the results of single-cell topological data analysis (scTDA) of motor neuron differentiation.