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Fast and accurate in silico inference of HLA genotypes from RNA-seq
Pipeline to infer recombination rates
Script of bootstrap analysis of evolution tree used in Juan M Arriaga, et al. A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nature Cancer (2020)
TOBI predicts somatic variants from .vcf or .bam input
Dockerfolder for Docker-ized version of SAVI
A Library for Denoising Single-Cell Data with Random Matrix Theory
MAGE - Multilevel Analysis of Gene Expression
An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data
The Medical Imaging Interaction Toolkit with augmented tools for segmentation (MITKats), an extension of MITK with Threshold Components and Clipping Segmentation features.
NORI (Non-coding RNA Identification), a computational tool to identify lncRNAs using next generation sequencing.
Implementation of Mapper Algorithm
Evolutionary Moduli space visualization and statistics
Topological inference of horizontal evolution from multiple sequence alignments
Annotation and Prediction of Oncogenic Gene Fusions in RNAseq
Persistent Homology Datasets
Code for "Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes". View more information in the ipython notebook
Tumor Only Boosting Identification of driver mutations.