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d3b-flywheel-routine-empty-containers

Routine QC job for data hosted on Flywheel

d3b-flywheel-routine-missing-classifications

routine QC job for data hosted on Flywheel

d3b-flywheel-warehousing

Warehousing from flywheel

d3b-imaging-deid

d3b-lib-pfb-exporter

🏭Transform and export data from a relational database to a PFB (Portable Format for Bioinformatics) Avro 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

d3b-pathogenicity-preprocessing

In collaboration with the Diskin lab, this repo houses a workflow designed to take in KF annotated vcf files, and further annotate for pathogenicity prediction

d3b-publication-code

Central repository to organize publication-related code

d3b-python-template

Template Python Repo for D3B Projects

d3b-redcap-api-python

⛑ REDCap API interface in Python

d3b-redcap-reporting

d3b-release-maker

🛠 Tool to generate GitHub-based software releases with semantic versioning tags

d3b-research-workflows

d3b-sftp-site

Configuration for AWS Transfer Family SFTP transfer server

d3b-supremo-dev

d3b-tpm-matrices

Repo to generate combined TPM matrices of various RNA-seq datasets

d3b-utils-python

Collection of reusable python utilities

d3b-warehouse-redcap

🏭 D3b Warehouse Pipeline for REDCap

d3b_bic-seq2

CWL Implementation based on this tool http://compbio.med.harvard.edu/BIC-seq/ and this cluster implementation : https://github.com/ding-lab/BICSEQ2

dang_mb_2020

Immune profiling for PBTA Medullo samples

dewrangle-python

diseasexpress-pipeline

pipeline to process diseaseXpress datasets

diseasexpress-rest-api

Rest API for disease express

diseasexpress-shinyapp

shinyapp for diseaseXpress

diseasexpress-web

docker-terraform

A base Docker image for Terraform.

dockerize

Utility to simplify running applications in docker containers

fusionannotator

FusionAnnotator source code

fw-captk-brats-pipeline

Flywheel gear for CaPTk-BraTSPipeline command

fw-captk-coregistration

Flywheel gear for CaPTk Preprocessing coregistration tool