Dirichlet Process based methods for subclonal reconstruction of tumours

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.

Lab Materials for MIT 6.S191: Introduction to Deep Learning

Official code repository for GATK versions 4 and up

Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

Mummer alignment tool

CS273B Deep Learning for Genomics Course Materials

Code accompanying "The evolutionary history of 2,658 cancers", bioRxiv

Inferring CNV from Single-Cell RNA-Seq

a snakemake pipeline to process ChIP-seq files from GEO or in-house

Long-Read Sequencing Workshop

An example package generated as a part of BIOSTAT615 lecture material

An example Rcpp package to read a VCF file

A comprehensive list of Deep Learning / Artificial Intelligence and Machine Learning tutorials - rapidly expanding into areas of AI/Deep Learning / Machine Vision / NLP and industry specific areas …

docker container for running NCI GDC gdc-client

identifying mutational significance in cancer genomes

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current …

Structural variation and indel detection by local assembly

ASCAT R package

Robust and efficient workflows using a simple language agnostic approach

Python implementation of mutual information calculation using B-spline from Daub et. al.