aminzia,Amin,github

dockerflow

Dockerflow is a workflow runner that uses Dataflow to run a series of tasks in Docker with the Pipelines API

gatk

GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses

gene_coverage

Calculates gene-level breadth-of-coverage at several depth-of-coverage thresholds.

genomegenerator

A tool that generates genomics datasets for BigQuery

haystackheuristic

Example Code for Carrying out the Haystack Heuristic on Sample Immunological Data

hugeseq

For original Nature Biotechnology Publication (Q1 2012)

immunarch

An R Package for Fast and Effortless Analysis of Large-Scale Immune Repertoire Data

manta

Structural variant/large-indel caller for Illumina paired-end sequencing reads

one-shot-learning-with-siamese-networks

Implementation of One Shot Learning using Convolutional Siamese Networks on Omniglot Dataset

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

pipelines-api-examples

Examples for the Google Genomics Pipelines API.

stanford-cs-230-deep-learning

VIP cheatsheets for Stanford's CS 230 Deep Learning

statgen

This repository has been deprecated and replaced with libStatGen, https://github.com/statgen/libStatGen and the tools have been broken out to other repositories including: https://github.com/statgen/bamUtil and https://github.com/statgen/qplot

stormseq

STORMSeq: Scalable Tools for Open-source Read Mapping

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

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