D3b's repositories
fw_download_gear_output
Python command to download analysis output from Flywheel using SDK
redcap-aws-cloudformation
This repository contains AWS CloudFormation templates to automatically deploy a REDCap environment that adheres to AWS architectural best practices
fw-captk-brats-pipeline
Flywheel gear for CaPTk-BraTSPipeline command
fw-change-seg-labels
Flywheel gear to change BRATS output segmentation labels
r-shiny-imaging-data-metrics
R Shiny App to query Flywheel data based on various clinical, scanner, and image properties, exports results to local file
d3b-ot-pdx-tumor-only-processing
Open Targets Tumor-only + PDX processing pipelines. Mostly a port over of the pipelines from https://cgc.sbgenomics.com/public/apps/q?search=pdx
keycloak-gims
Keycloak Deployment for GIMS(UCSF) project
cavatica_airflow_plugins
Operators, Sensors, and other plugins for working with Cavatica via Airflow
d3b-redcap-api-python
⛑ REDCap API interface in Python
diseaseXpress-rest-api
Rest API for disease express
resource-auto-tagger
WARNING - This package is no longer supported. Source code & IAM policies for AWS Lambda function described in "Automatically tag new AWS resources based on identity or role" blog post.
aws-cost-explorer-report
Python SAM Lambda module for generating an Excel cost report with graphs, including month on month cost changes. Uses the AWS Cost Explorer API for data.
tiru-internal-data-ingest-local
Pipeline to transfer data from Orthanc to Flywheel
d3b-publication-code
Central repository to organize publication-related code
fw-fsl-slicesdir
Flywheel gear for FSL slicesdir command
tiru-preproc-mri
Preprocessing code for MR images (uses CaPTk/BRATS pipeline).
dockerize
Utility to simplify running applications in docker containers
gene_lists
List of gene lists for genomic analyses.
clinical-data-flow
📓Project management and design artifacts for Clinical Data Flow
d3b-dev-rnaseq-snv
RNAseq SNV Calling Workflow (beta). This workflow follows the COV-IRT NASA-developed pipeline, with the exception of joint genotyping-specific params and steps.
medullo-classifier-dev
Repo to train the classifier and test it on 15 datasets
d3b-tpm-matrices
Repo to generate combined TPM matrices of various RNA-seq datasets
d3b-lib-pfb-exporter
🏭Transform and export data from a relational database to a PFB (Portable Format for Bioinformatics) Avro file
controlfreec_cnv
Re-develop/redeploy our controlfreec tool to include exome mode