Links to Useful
Resources & Software
Useful Software
Please note that the following software projects may be in active development & varying stages of usability.
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arcasHLA is a tool for in silico inference of HLA genotypes (MHC class 1 and class 2) from RNA-seq.
link: arcasHLA
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Randomly is a python package for denoising single cell data with random matrix theory.
link: Randomly
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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
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mutcomfocal is a tool for identifying recurrent and focal genomic alterations in tumor samples described in this publication.
link: mutcomfocal
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Pancancer is a web app to explore genetic alterations in TCGA (The Cancer Genome Atlas) using Topological Data Analysis.
link: Pancancer
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Primate Marburg Infection Gene Expression Explorer is a web app for exploring the gene expression of primates infected with Marburg virus.
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Pegasus is a tool for the annotation and prediction of oncogenic gene fusions in RNAseq.
link: Pegasus
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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
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Exotome Browser is a locally hosted implementation of the UCSC Genome Browser for browsing the mm9 exotome described in this publication.
link: Exotome Browser
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scTDA is an object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data.
link: scTDA
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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
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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