d3b-center/d3b-analysis-toolkit

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Python
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Apache License 2.0
Created over 3 years ago
Updated almost 2 years ago

d3b-center/d3b-analysis-toolkit

d3b-center

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CNS Tumor Subtyping Project. Currently in beta development!

annoFuse

Filter and prioritize fusion calls

bixtools

🐳 Dockerfiles for bioinformatics tools

PBTA-ALT-analysis

Repository for CBTTC-ALT project with Kristina Cole

d3b-utils-python

Collection of reusable python utilities

peds-brain-auto-seg-public

D3b PedsBrainAutoSeg tool (public realease)

medullo-classifier-package

R package for Medulloblastoma subtype classification

celllines-profiling-analysis

Stemness analysis in HGG Suspension vs Adhesion cell lines

hope-cohort-analysis

Analysis for HOPE cohort

d3b-redcap-api-python

⛑ REDCap API interface in Python

tiru-preproc-mri

Preprocessing code for MR images (uses CaPTk/BRATS pipeline).

d3b-research-workflows

Common Workflow Language

ticket-tracker-OPC

A repo to generate and track tickets for ped OT

OMPARE

OMics PAtient REport

image-deid-etl

A WIP tool to assist with reading DICOM images from Orthanc, conversion to anonymized NIfTI images, and uploading to Flywheel.

d3b-adapt-query-library

Storage for ADAPT SQL queries

peds-brain-seg-pipeline-public

Preprocessing and automatic tumor segmentation for pediatric brain tumor subjects

d3b-cds-manifest-prep

scripts to prep manifests for cds

d3b-python-template

Template Python Repo for D3B Projects

OpenPedCan-manuscript

The manuscript repository for the Pediatric Open Targets Project

pbta-splicing

Splicing analysis across the PBTA

pbta-ancestry

medullo-classifier-shinyapp

Shiny app for medullo classifier R package

PBTA-miRNA-analysis

Analysis of PBTA miRNA data

d3b-publication-code

Central repository to organize publication-related code

tumor-loh-app-dev

Development repo for LOH

diseaseXpress-pipeline

pipeline to process diseaseXpress datasets

bix-molecular-subtyping

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.

pediatric-auto-defacer-public

Release of trained pediatric defacing tool for MRI files

peds-brain-tumor-preproc

Docker for pre-processing module