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funnel
Funnel is a toolkit for distributed task execution via a simple, standard API.g2p-aggregator
Associations of genomic features, drugs and diseasescwl-tes
cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible.dos_connect
Data Object Registry Connectdockerized-tools
tesseract
Python lib for remote code execution via the GA4GH TES APIcompbio-galaxy-wrappers
OHSU Galaxy wrappers.py-tes
Python SDK for the GA4GH Task Execution APIwdl-pcawg-bwa-mem-workflow
WDL implementation of https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflowgdc-scan
A library for navigating and downloading from the GDC APIbcc
LabKey module for Brenden-Colson CenterR-utils
R utilities for omic analysesgen3_etl
load gen3 with project datawdl-pcawg-sanger-cgp-workflow
WDL implementation of https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Dockervariant_store_docker
mIHC-ML
Machine learning for mIHCbridge2ai-jupyter
Docker Image for JupyterHub with restricted download and tensorflow/pytorchhomebrew-formula
homebrew tap for OHSU Comp Bio toolsohsu-comp-bio.github.io
ohsu-comp-bio.github.io website.cellpose_segmentation
Galaxy tool for for cell and nucleus segmentation using Cellposefunnel-compliance
GA4GH TES compliance status of the Funnel toolkitaracne
Wrapper scripts for Aracne-AP, "Network Reverse Engineering through AP inference of Mutual Information"common_workflow_language_schema
Jsonnet documents for building a Common Workflow Language Avro protocolopenstack_k8s
Utilities to provision kubernetes clusters in an on premises openstack environment.ceph-docker-compose
viper
Wrapper scripts for viper's network regulator analysis and reporting.scimap_phenotyping
Galaxy tool wrappers for single cell phenotyping analysis using Scimap, Squidpy, Vitessce etc.bergamot
hapi-fhir-auth
HAPI FHIR authorization hook for the ACED data commonsgaia_mutex_integration
scRNA_cell_type
CellO using seurat objectsrandom-pipeline-scripts
Pipeline descriptions and scripts taken from the web.neoepitope_novelty
Tools for annotating neoepitope predictions for focus on peptide noveltydrake-demo
A sample Drake workflowAnVIL-FHIR
FHIR schema for AnVIL projectsdata-import-test
Collection of scripts and documentation for importing S3 data into the Gen3 systemrockefeller_metabolomics
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