D3b
Center for Data Driven Discovery in Biomedicine at the Children's Hospital of Philadelphia
Philadelphia, PA
Pinned Repositories
annoFuse
Filter and prioritize fusion calls
bixtools
🐳 Dockerfiles for bioinformatics tools
celllines-profiling-analysis
Stemness analysis in HGG Suspension vs Adhesion cell lines
d3b-cli-igor
All-purpose CLI tool for D3b Center and partner orgs
d3b-utils-python
Collection of reusable python utilities
medullo-classifier-package
R package for Medulloblastoma subtype classification
OpenPedCan-analysis
The analysis repository for the Open Pediatric Cancer Project
PBTA-ALT-analysis
Repository for CBTTC-ALT project with Kristina Cole
pedcbioportal
cBioPortal for Cancer Genomics
peds-brain-auto-seg-public
D3b PedsBrainAutoSeg tool (public realease)
D3b's Repositories
d3b-center/annoFuse
Filter and prioritize fusion calls
d3b-center/OpenPedCan-analysis
The analysis repository for the Open Pediatric Cancer Project
d3b-center/bixtools
🐳 Dockerfiles for bioinformatics tools
d3b-center/peds-brain-auto-seg-public
D3b PedsBrainAutoSeg tool (public realease)
d3b-center/hope-cohort-analysis
Analysis for HOPE cohort
d3b-center/image-deid-etl
A WIP tool to assist with reading DICOM images from Orthanc, conversion to anonymized NIfTI images, and uploading to Flywheel.
d3b-center/peds-brain-seg-pipeline-public
Preprocessing and automatic tumor segmentation for pediatric brain tumor subjects
d3b-center/OpenPedCan-manuscript
The manuscript repository for the Pediatric Open Targets Project
d3b-center/pbta-ancestry
d3b-center/pbta-splicing
Aberrant splicing in DMG
d3b-center/pediatric-auto-defacer-public
Release of trained pediatric defacing tool for MRI files
d3b-center/peds-brain-tumor-preproc
Docker for pre-processing module
d3b-center/d3b-cli-igor
All-purpose CLI tool for D3b Center and partner orgs
d3b-center/d3b-dff-cli
the command line tool code base for d3b data file foundation
d3b-center/pLGG-immune-clinicoradiomics
d3b-center/pLGG_imaging_clustering_genomic
d3b-center/annoFuseData
d3b-center/canine-dev
Canine WF development
d3b-center/cbioportal
cBioPortal for Cancer Genomics
d3b-center/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-center/d3b-sftp-site
Configuration for AWS Transfer Family SFTP transfer server
d3b-center/fw-captk-preproc-zscore-norm
Flywheel gear implementing CaPTk's Preprocessing Z-score Normalization
d3b-center/fw-fsl-fast
Flywheel gear to implement FSL's FAST tool
d3b-center/fw-geojson2image
Flywheel gear to create a labeled image from a QuPath GeoJSON
d3b-center/fw-histomicsTK-feature-extraction
Flywheel gear for generating pathomic features
d3b-center/fw-histomicsTK-tile-wsi
Flywheel gear to extract tiles of a whole slide image (HistomicsTK/large_image)
d3b-center/HLA-Typing-Dev
HLA Typing development space. Testing and benching various tools
d3b-center/peds-brain-auto-skull-strip
Docker for automated skull stripping for pediatric brain tumor subjects
d3b-center/Playbook-Workflow-Builder
A repository for the Playbook Workflow Builder project.
d3b-center/terraform-aws-vpc
A Terraform module to create a dual-stack (IPv4/IPv6) Amazon Web Services (AWS) Virtual Private Cloud (VPC).