Repositories list

• CARE_IMPACT_analysis_for_manuscript

  Public
  Work supporting the manuscript submission effort underway July 2023

  HTML

  •0•0•5•0•Updated Jan 27, 2025Jan 27, 2025

• mend_qc

  Public
  Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file

  sambambamendrseqc+ 2samblasterdocker

  R

  •

  MIT License

  •0•4•1•2•Updated Jan 13, 2025Jan 13, 2025

• shell-novice2

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

• shell-novice

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• brca-exchange

  Public
  Overall management and deployment of the BRCA Exchange web portal and pipeline scripts

  Python

  •32•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• compendium-expression-matrix

  Public
  Python

  •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

• ccdi-federation-api

  Public
  0•0•0•0•Updated May 17, 2024May 17, 2024

• TUBI-Manuscript-1

  Public
  HTML

  •

  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Oct 13, 2023Oct 13, 2023

• TUBI-Manuscript

  Public
  0•0•0•0•Updated Oct 5, 2023Oct 5, 2023

• hbtest_OpenPBTA-manuscript

  Public
  The manuscript repository for the Open Pediatric Brain Tumor Atlas Project

  HTML

  •

  Other

  •26•0•0•0•Updated Aug 30, 2023Aug 30, 2023

• TUBI-2023

  Public
  HTML

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Aug 30, 2023Aug 30, 2023

• hexmap-data

  Public
  compute server for hexmap

  Python

  •1•0•0•0•Updated Aug 17, 2023Aug 17, 2023

• hexmap-view

  Public
  JavaScript

  •

  MIT License

  •3•0•0•0•Updated Aug 17, 2023Aug 17, 2023

• pipelines

  Public
  Makefiles to run dockerized pipelines used in Treehouse on a single sample

  Makefile

  •

  Apache License 2.0

  •6•3•11•0•Updated Aug 9, 2023Aug 9, 2023

• CARE

  Public
  Treehouse Comparative Analysis of RNA Expression

  Jupyter Notebook

  •

  Apache License 2.0

  •0•2•2•2•Updated May 8, 2023May 8, 2023

• TumorMap_Cluster_Analysis

  Public
  Code for analyzing how samples clusters in the Treehouse TumorMap

  0•0•0•0•Updated Mar 9, 2023Mar 9, 2023

• archive

  Public
  Scripts facilitating the Treehouse storage management

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 16, 2022Dec 16, 2022

• mini-var-call

  Public
  Calls and annotates a small curated list of variants from a sorted bam file

  Python

  •0•0•0•0•Updated Oct 28, 2022Oct 28, 2022

• fusion-for-core

  Public
  UCSC Treehouse Gene Fusion Analysis Pipeline

  Python

  •9•1•0•0•Updated Oct 26, 2022Oct 26, 2022

• OpenPBTA-manuscript

  Public
  The manuscript repository for the Open Pediatric Brain Tumor Atlas Project

  HTML

  •

  Other

  •26•0•0•0•Updated Aug 29, 2022Aug 29, 2022

• dngds-pipelines

  Public
  DNA Nanopore Genetic Disease Study

  Makefile

  •

  Apache License 2.0

  •2•0•0•1•Updated Jul 26, 2022Jul 26, 2022

• epinano_support

  Public
  Dockerfile

  •

  Apache License 2.0

  •0•0•0•0•Updated Jul 19, 2022Jul 19, 2022

• transcript2genome_coords

  Public
  Apache License 2.0

  •0•0•0•0•Updated Jul 18, 2022Jul 18, 2022

• no-toil-rnaseq

  Public
  Shell

  •1•0•0•0•Updated Jun 10, 2022Jun 10, 2022

• protect

  Public
  Python

  •

  Apache License 2.0

  •13•0•0•0•Updated Apr 27, 2022Apr 27, 2022

• receiving

  Public
  As simple as possible, but no simpler, browser upload to S3

  JavaScript

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  Apache License 2.0

  •1•0•0•0•Updated Apr 21, 2021Apr 21, 2021

• MEND_qc_survey

  Public
  HTML

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  MIT License

  •0•0•2•0•Updated Feb 22, 2021Feb 22, 2021

• xenahub

  Public
  Stand-alone Dockerized Xena Hub

  Dockerfile

  •3•0•0•0•Updated Feb 1, 2021Feb 1, 2021

• gene_expression_outlier_accuracy

  Public
  HTML

  •2•0•0•0•Updated Aug 27, 2020Aug 27, 2020

• EMT-paper

  Public
  Code for creating figures for Sanders, L.M., Cheney, A., et al., "Identification of a differentiation stall in epithelial mesenchymal transition in histone H3 mutant diffuse midline glioma"

  Jupyter Notebook

  •1•0•0•0•Updated Aug 17, 2020Aug 17, 2020