D3b's repositories
OpenPedCan-analysis
The analysis repository for the Open Pediatric Cancer Project
hope-cohort-analysis
Analysis for HOPE cohort
peds-brain-auto-seg-public
D3b PedsBrainAutoSeg tool (public realease)
peds-brain-seg-pipeline-public
Preprocessing and automatic tumor segmentation for pediatric brain tumor subjects
d3b-python-template
Template Python Repo for D3B Projects
image-deid-etl
A WIP tool to assist with reading DICOM images from Orthanc, conversion to anonymized NIfTI images, and uploading to Flywheel.
OpenPedCan-manuscript
The manuscript repository for the Pediatric Open Targets Project
peds-auto-defacing-public
Release of trained pediatric defacing tool for MRI files
peds-brain-tumor-preproc
Docker for pre-processing module
ambra-code
Code examples for all things Ambra Health
d3b-cli-igor
All-purpose CLI tool for D3b Center and partner orgs
cbioportal
cBioPortal for Cancer Genomics
cbioportal-core
Externalized cBioPortal Core
d3b-dff-cli
the command line tool code base for d3b data file foundation
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-release-maker
🛠 Tool to generate GitHub-based software releases with semantic versioning tags
d3b-sftp-site
Configuration for AWS Transfer Family SFTP transfer server
fw-deepliif-compute-scores
Flywheel gear to compute scores for DeepLIIF IHC predictions
fw-deepliif-predict
Flywheel gear to implement DeepLIIF for IHC images
fw-gear-extract-slide-metadata
Flywheel gear to extract pathology slide metadata using OpenSlide
fw-histomicsTK-tile-wsi
Flywheel gear to extract tiles of a whole slide image (HistomicsTK/large_image)
HLA-Typing-Dev
HLA Typing development space. Testing and benching various tools
OpenPedCan-workflows
Upstream CWL workflows for OpenPedCan
peds-brain-auto-skull-strip
Docker for automated skull stripping for pediatric brain tumor subjects
terraform-aws-vpc
A Terraform module to create a dual-stack (IPv4/IPv6) Amazon Web Services (AWS) Virtual Private Cloud (VPC).