ohsu-comp-bio/AnVIL-FHIR

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Updated over 4 years ago

ohsu-comp-bio/AnVIL-FHIR

ohsu-comp-bio

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FHIR schema for AnVIL projects

funnel

Funnel is a toolkit for distributed task execution via a simple, standard API.

g2p-aggregator

Associations of genomic features, drugs and diseases

cwl-tes

cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible.

dos_connect

Data Object Registry Connect

dockerized-tools

tesseract

Python lib for remote code execution via the GA4GH TES API

compbio-galaxy-wrappers

OHSU Galaxy wrappers.

py-tes

Python SDK for the GA4GH Task Execution API

wdl-pcawg-bwa-mem-workflow

WDL implementation of https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow

gdc-scan

A library for navigating and downloading from the GDC API

bcc

LabKey module for Brenden-Colson Center

R-utils

R utilities for omic analyses

gen3_etl

load gen3 with project data

wdl-pcawg-sanger-cgp-workflow

WDL implementation of https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker

variant_store_docker

mIHC-ML

Machine learning for mIHC

Jupyter Notebook

bridge2ai-jupyter

Docker Image for JupyterHub with restricted download and tensorflow/pytorch

homebrew-formula

homebrew tap for OHSU Comp Bio tools

ohsu-comp-bio.github.io

ohsu-comp-bio.github.io website.

cellpose_segmentation

Galaxy tool for for cell and nucleus segmentation using Cellpose

funnel-compliance

GA4GH TES compliance status of the Funnel toolkit

aracne

Wrapper scripts for Aracne-AP, "Network Reverse Engineering through AP inference of Mutual Information"

Galaxy-ML

Make machine learning simpler with Galaxy (Moved to https://github.com/goeckslab/Galaxy-ML)

Jupyter Notebook

common_workflow_language_schema

Jsonnet documents for building a Common Workflow Language Avro protocol

openstack_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 commons

gaia_mutex_integration

scRNA_cell_type

CellO using seurat objects

random-pipeline-scripts

Pipeline descriptions and scripts taken from the web.

neoepitope_novelty

Tools for annotating neoepitope predictions for focus on peptide novelty

drake-demo

A sample Drake workflow

data-import-test

Collection of scripts and documentation for importing S3 data into the Gen3 system

rockefeller_metabolomics