wisekh6

dpclust

Dirichlet Process based methods for subclonal reconstruction of tumours

JaBbA

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

ecSeg

introtodeeplearning

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

gatk

Official code repository for GATK versions 4 and up

hmmcopy_utils

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

ichorCNA

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

mummer

Mummer alignment tool

cs273b

CS273B Deep Learning for Genomics Course Materials

PCAWG-11

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

infercnv

Inferring CNV from Single-Cell RNA-Seq

pyflow-ChIPseq

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

long-read-workshop

Long-Read Sequencing Workshop

hmm615

An example package generated as a part of BIOSTAT615 lecture material

tinyVcfReader

An example Rcpp package to read a VCF file

Artificial-Intelligence-Deep-Learning-Machine-Learning-Tutorials

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 such as Climate / Energy, Automotives, Retail, Pharma, Medicine, Healthcare, Policy, Ethics and more.

gdc-client

docker container for running NCI GDC gdc-client

MuSiC2

identifying mutational significance in cancer genomes

AmpliconArchitect

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 version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.

svaba

Structural variation and indel detection by local assembly

circleseq

ascat

ASCAT R package

flowr

Robust and efficient workflows using a simple language agnostic approach

pymi

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