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 10 593
bixtools
🐳 Dockerfiles for bioinformatics tools
Language:Dockerfile15 8 44
celllines-profiling-analysis
Stemness analysis in HGG Suspension vs Adhesion cell lines
Language:R3 7 20
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 7 42
OpenPedCan-analysis
The analysis repository for the Open Pediatric Cancer Project
Language:HTML16 6 9614
PBTA-ALT-analysis
Repository for CBTTC-ALT project with Kristina Cole
Language:HTML4 5 150
pedcbioportal
cBioPortal for Cancer Genomics
Language:JavaScript31
peds-brain-auto-seg-public
D3b PedsBrainAutoSeg tool (public realease)
6 5 10

D3b's Repositories

d3b-center/d3b-app-fhir-etl
Language:Python
d3b-center/bixu-shinyapp-cloud-credit-billing-group
Language:R
d3b-center/celllines-profiling-analysis
Stemness analysis in HGG Suspension vs Adhesion cell lines
Language:R3
d3b-center/fw-captk-whitestripe-normalization
fw-captk-whitestripe-normalization
Language:Shell
d3b-center/D3b-autoPVS1
This is a modiifed port of the original https://github.com/JiguangPeng/autopvs1, branched from commit `7fb1be97667e5ef576f81bf2fabbddcf9a4c7594`. It was re-worked in order to work with Kids First germline annotation outputs.
Language:Python21
d3b-center/fw-copy-preproc-files-2-acq
Flywheel SDK gear to copy pre-processed files & rename them
Language:Python
d3b-center/fw-captk-n4-bias-correction
Flywheel gear that implements N4 bias correction of an image
Language:Shell
d3b-center/d3b-cds-manifest-prep
scripts to prep manifests for cds
Language:Python1
d3b-center/fw-captk-feature-extraction
Flywheel gear that implements CaPTk feature extraction tool
Language:Shell
d3b-center/fw-intensity-rescale-winsorize
Flywheel gear to rescale and winsorize signal intensities of an input image
Language:Python
d3b-center/test-transfer-repo
d3b-center/fw-fsl-slicer
Flywheel gear for FSL slicer command
Language:Shell
d3b-center/fw_classification_profiles
YAML profiles for Flywheel's file-classifier gear
Language:Python
d3b-center/medullo-classifier-package
R package for Medulloblastoma subtype classification
Language:R32
d3b-center/fw-dynamic-range-mri
Flywheel gear to calculate the dynamic range of an MRI
Language:Python
d3b-center/fw-qc-migrate-segmentation-files
Language:Python
d3b-center/fw-captk-histogram-matching
Flywheel gear to implement CaPTk histogram matching tool
Language:Shell
d3b-center/ucsf-portal
Language:TypeScript1
d3b-center/d3b-flywheel-routine-empty-containers
Routine QC job for data hosted on Flywheel
Language:Python
d3b-center/d3b-bixu-template
d3b-center/d3b-arcus-manifest-prep
🗃️ tool to generate manifests for transfering cbtn data to arcus
Language:Python
d3b-center/ucsf-riff
Riff Application for UCSF deployment
Language:TypeScript
d3b-center/d3b-bixu-data-assembly
Language:HTML
d3b-center/fw-captk-diffusion-derivatives
Flywheel gear that implements CaPTk Diffusion Derivatives tool
Language:Shell
d3b-center/toolkit-resources
The purpose of this repo is to make regularly updated resource files available to the d3b-analysis-toolkit and to track changes to these files
d3b-center/ticket-tracker-OPC
A repo to generate and track tickets for ped OT
2
d3b-center/d3b-cavatica-python-tools
Collection of python tools for interacting with the cavatica API
Language:Python
d3b-center/fw-captk-coregistration
Flywheel gear for CaPTk Preprocessing coregistration tool
Language:Shell
d3b-center/d3b-utils-python
Collection of reusable python utilities
Language:Python4
d3b-center/d3b-warehouse-redcap
🏭 D3b Warehouse Pipeline for REDCap
Language:Python