Explore @BD2KGenomics Open Source projects

UC Santa Cruz Genomics Institute - Computational Genomics Lab (@BD2KGenomics)

BD2KGenomics

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303
Global Org. Rank 32,143 (Top 11 %)
Registered about 10 years ago
Most used languages

Python
62.5 %

Shell
15.0 %

Common Workflow Language 7.5 %

JavaScript
5.0 %

Scala
2.5 %

Protocol Buffer 2.5 %

R
2.5 %

Jupyter Notebook
2.5 %
Location 🇺🇸 United States
Country Total Rank 21,598
Country Ranking

Common Workflow Language 17

Protocol Buffer 55

Scala
863

Python
5,296

R
6,924

Shell
7,800

Jupyter Notebook
9,731

toil-rnaseq

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline

toil-scripts

Toil workflows for common genomic pipelines

protect

cgcloud

Image and VM management for Jenkins, Spark and Mesos clusters in EC2

cgl-docker-lib

conductor

Efficient, distributed downloads of large files from S3 to HDFS using Spark.

s3am

A fast, parallel, streaming multipart uploader for S3

hgvm-graph-bakeoff-evaluations

All code for reproducing reference graph bakeoff results

bioapi-examples

Code examples for working with web based bioinformatics APIs

Jupyter Notebook

brca-website-deprecated

This repo is deprecated! Please use https://github.com/BD2KGenomics/brca-exchange

23andMe-brca-exchange

Get expert, curated information about your 23andMe results in the BRCA1 and 2 regions

toil-lib

A common library for functions and tools used in toil-based pipelines

bd2k-python-lib

The BD2K Python module kitchen sink

brca-pipeline

This repo is deprecated! Please use https://github.com/BD2KGenomics/brca-exchange

dcc-metadata-indexer

Scripts and schemas for JSON documents used with the DCC storage system and for building Elasticsearch indexes

core-operations

test repo for core operation

hgvm-builder

Tool to build a (Human) Genome Variation Map from a set of data sources

adam-contest-eval

Run ADAM variant calling against the 1000genomes.org dataset

vcf-to-ga

Generates GA4GH messages from VCF data

dockstore_tool_adtex

dcc-redwood-client

dockstore_workflow_fusion

Runs STARFusion and arriba

Common Workflow Language

10k-exomes

toil-rnaseq-sc

Toil-based RNA-seq pipeline for processing single-cell data

dockstore_workflow_snps

Workflow for variant callers MuSE, MuTect, SomaticSniper, and Pindel

Common Workflow Language

dockstore_tool_varscan_cnv

Varscan copynumber variation caller workflow

toil-topmed

The repository for the Toil TOPMed alignment best practice workflow.

dcc-ops

The UCSC Genomics Institute's Computational Genomics Platform (CGP). This repo contains the Docker compose-based deployment process.

hgvm

toil-workflows

Modern Toil Workflows

Common Workflow Language

ga4gh-gemini

Providing a GA4GH Interface to Gemini Variant Data

Protocol Buffer

hgvm-aligner-bakeoff-compliance

Tools and specifications for aligner behavior in the graph aligner bake-off

ga4gh-integration-deprecated

Tracking for ga4gh-integration projects

false-tandem-dup-finder

Scripts to find false tandem dups around scaffold gaps

dockstore_workflow_cnv

Runs ADTEx and Varscan copynumber on input exome bam files

dcc-feature-requests

Add feature requests for the UCSC GI Computational Platform here

cgl-hr

A public wiki for open projects in the CGL lab

driver-projects

DREAMChallenges

a place to track work on the GA4GH Dream Challenges

platform-administration

Issues representing platform epics, user stories, tasks, etc. that are not specific to an existing component repository.

fhir-ga4gh-integration

Improve integration of FHIR Genomics and GA4GH

dcc-spinnaker-client

The submission system client that uploads data/metadata to Redwood and indicates to the Spinnaker web service that a submission bundle is ready for validation.

dcc-metadata-schemas

Repository for our JSON schema's used to describe our common metadata model.

dcc-redwood-compose

dockstore_tool_arriba

Implementation of structural variant finding algorithm arriba by Sebastian Uhrig

dcc-spinnaker

The server web service and UI for interacting with the Spinnaker validation system.

dcc-auth-proxy

Proxy in front of dcc services ensuring the right people are passed through with the right privileges

parasol-binaries

A stop-gap for hosting parasol binaries. If in doubt, ignore this.

dcc-action-service

A place for our business logic written in Luigi that triggers workflow launches.

dockstore-tool-gene-by-cell-creator

creates a gene by cell matrix from multiple slices

dcc-dockstore-tool-runner

A Dockstore tool designed to perform file downloads from Redwood, run another Dockstore tool, and then upload to Redwood.