Links to Useful

Resources & Software

 
 

Useful Software

Please note that the following software projects may be in active development & varying stages of usability.

  • 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