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
Language:R20 10 553
bixtools
🐳 Dockerfiles for bioinformatics tools
Language:Dockerfile14 8 44
celllines-profiling-analysis
Stemness analysis in HGG Suspension vs Adhesion cell lines
Language:R30
d3b-cli-igor
All-purpose CLI tool for D3b Center and partner orgs
Language:Python00
d3b-utils-python
Collection of reusable python utilities
Language:Python4 9 40
medullo-classifier-package
R package for Medulloblastoma subtype classification
Language:R3 8 42
OpenPedCan-analysis
The analysis repository for the Open Pediatric Cancer Project
Language:HTML15 6 7013
PBTA-ALT-analysis
Repository for CBTTC-ALT project with Kristina Cole
Language:HTML4 6 150
pedcbioportal
cBioPortal for Cancer Genomics
Language:JavaScript31
peds-brain-auto-seg-public
D3b PedsBrainAutoSeg tool (public realease)
40

D3b's Repositories

d3b-center/annoFuse
Filter and prioritize fusion calls
Language:R20 10 553
d3b-center/OpenPedCan-analysis
The analysis repository for the Open Pediatric Cancer Project
Language:HTML15 6 7013
d3b-center/bixtools
🐳 Dockerfiles for bioinformatics tools
Language:Dockerfile14 8 44
d3b-center/peds-brain-auto-seg-public
D3b PedsBrainAutoSeg tool (public realease)
40
d3b-center/hope-cohort-analysis
Analysis for HOPE cohort
Language:HTML3 6 431
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.
Language:Python2
d3b-center/peds-brain-seg-pipeline-public
Preprocessing and automatic tumor segmentation for pediatric brain tumor subjects
2
d3b-center/OpenPedCan-manuscript
The manuscript repository for the Pediatric Open Targets Project
Language:HTML13
d3b-center/pbta-ancestry
Language:HTML1
d3b-center/pbta-splicing
Aberrant splicing in DMG
Language:HTML1
d3b-center/pediatric-auto-defacer-public
Release of trained pediatric defacing tool for MRI files
1
d3b-center/peds-brain-tumor-preproc
Docker for pre-processing module
Language:Python1
d3b-center/d3b-cli-igor
All-purpose CLI tool for D3b Center and partner orgs
Language:Python00
d3b-center/d3b-dff-cli
the command line tool code base for d3b data file foundation
Language:Python0 5 00
d3b-center/pLGG-immune-clinicoradiomics
Language:Jupyter Notebook0 6 20
d3b-center/pLGG_imaging_clustering_genomic
Language:HTML00
d3b-center/annoFuseData
Language:R
d3b-center/canine-dev
Canine WF development
Language:Common Workflow Language
d3b-center/cbioportal
cBioPortal for Cancer Genomics
Language:Java
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
Language:Common Workflow Language
d3b-center/d3b-sftp-site
Configuration for AWS Transfer Family SFTP transfer server
Language:HCL5 0
d3b-center/fw-captk-preproc-zscore-norm
Flywheel gear implementing CaPTk's Preprocessing Z-score Normalization
Language:Shell
d3b-center/fw-fsl-fast
Flywheel gear to implement FSL's FAST tool
Language:Shell
d3b-center/fw-geojson2image
Flywheel gear to create a labeled image from a QuPath GeoJSON
Language:Python
d3b-center/fw-histomicsTK-feature-extraction
Flywheel gear for generating pathomic features
Language:Python
d3b-center/fw-histomicsTK-tile-wsi
Flywheel gear to extract tiles of a whole slide image (HistomicsTK/large_image)
Language:Python
d3b-center/HLA-Typing-Dev
HLA Typing development space. Testing and benching various tools
Language:Python
d3b-center/peds-brain-auto-skull-strip
Docker for automated skull stripping for pediatric brain tumor subjects
Language:Python
d3b-center/Playbook-Workflow-Builder
A repository for the Playbook Workflow Builder project.
Language:TypeScript
d3b-center/terraform-aws-vpc
A Terraform module to create a dual-stack (IPv4/IPv6) Amazon Web Services (AWS) Virtual Private Cloud (VPC).
Language:HCL7 0