Pinned Repositories
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
koalatea
Quality control pipeline
labs
Scripts for HarvardX courses: PH525x
manta
Structural variant/large-indel caller for Illumina paired-end sequencing reads
aminzia's Repositories
aminzia/dockerflow
Dockerflow is a workflow runner that uses Dataflow to run a series of tasks in Docker with the Pipelines API
aminzia/gatk
GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses
aminzia/gene_coverage
Calculates gene-level breadth-of-coverage at several depth-of-coverage thresholds.
aminzia/GenomeGenerator
A tool that generates genomics datasets for BigQuery
aminzia/HaystackHeuristic
Example Code for Carrying out the Haystack Heuristic on Sample Immunological Data
aminzia/HugeSeq
For original Nature Biotechnology Publication (Q1 2012)
aminzia/immunarch
An R Package for Fast and Effortless Analysis of Large-Scale Immune Repertoire Data
aminzia/koalatea
Quality control pipeline
aminzia/labs
Scripts for HarvardX courses: PH525x
aminzia/manta
Structural variant/large-indel caller for Illumina paired-end sequencing reads
aminzia/One-Shot-Learning-with-Siamese-Networks
Implementation of One Shot Learning using Convolutional Siamese Networks on Omniglot Dataset
aminzia/pindel
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.
aminzia/pipelines-api-examples
Examples for the Google Genomics Pipelines API.
aminzia/stanford-cs-230-deep-learning
VIP cheatsheets for Stanford's CS 230 Deep Learning
aminzia/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
aminzia/stormseq
STORMSeq: Scalable Tools for Open-source Read Mapping
aminzia/vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms