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antlr4

ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files.

atlas

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

cbioportal

cbioportal-docker

A context to create cBioPortal docker images

cbioportal-gsva-analysis

GSVA score and p-value calculation for TCGA studies in cBioPortal

cbioportal-pipelines

civic-server

Backend Server for CIViC Project

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

data_pipeline-1

Code for the data processing pipeline

datahub

A centralized location for storing curated data ready for inclusion in cBioPortal.

dcc-portal

Data portal for exploring and accessing data

gatk

Official code repository for GATK versions 4 and up

genesis

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

genetics

Issue tracker for Open Targets Genetics

genetics-pipe

genome-nexus

Interpreting cancer genomics data

genome-nexus-importer

Import data into MongoDB for use by https://github.com/genome-nexus/genome-nexus/

genomederiveddiagnosis

gscf

Generic Study Capture Framework

hannibal-luigi

opentargets luigi workflows

json_schema

Open Targets target-disease association schema

jstat

JavaScript Statistical Library

ksg_web

KSG Public Web Site

manta

Structural variant and indel caller for mapped sequencing data

mermaid

Generation of diagrams like flowcharts or sequence diagrams from text in a similar manner as markdown

mzidlib

MzidLib - A library of routines for manipulating data in the PSI's mzIdentML standard. ProteoAnnotator is a completely automated software pipeline for integration of mass spectrometry (MS) based proteomic evidence into genome databases.

ohdsi-etl-synthea

Conversion from Synthea CSV to OMOP CDM

ontoma

Map your disease and phenotype terms to the Open Targets platform ontology

opal

OBiBa’s core database application for biobanks or epidemiological studies.