Resources & Software

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

link: arcasHLA

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

link: Randomly

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.

link: cancerdrugexplorer.org

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

link: mutcomfocal

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

link: Pancancer

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

link: Primate Marburg Infection Gene Expression Explorer 

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

link: Pegasus

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.

link: GAMToC

Exotome Browser is a locally hosted implementation of the UCSC Genome Browser for browsing the mm9 exotome described in this publication.

link: Exotome Browser

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

link: scTDA

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.

link: TARGet

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

link: Motor Neurons scTDA