Skip to content

@UCSC-Treehouse UCSC Treehouse Childhood Cancer Initiative

Change the repository type filter

All

    Repositories list

    57 repositories

    • mend_qc

      Public
      Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file
      dockersambambamend
      dockersambambamendrseqcsamblaster
      R
      •
      MIT License
      •1•4•1•2•Updated Apr 24, 2026Apr 24, 2026

    • lib-prep-visualization

      Public
      Visualization tool for comparing RNA-seq expression data across different library preparation methods using UMAP.
      Python
      •
      MIT License
      •0•0•1•0•Updated Mar 18, 2026Mar 18, 2026

    • Essential-skills-for-Treehouse-computational-research

      Public
      To begin, start with the README displayed on this page.
      R
      •3•0•39•15•Updated Dec 3, 2025Dec 3, 2025

    • Siga2Essential-skills-for-Treehouse-computational-research

      Public
      To begin, start with the README displayed on this page.
      R
      •3•0•0•0•Updated Sep 20, 2025Sep 20, 2025

    • deseq2_practice_grzc

      Public
      0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • connerrobinson_essential_skills_in_computational_research

      Public
      R
      •0•0•1•11•Updated Aug 25, 2025Aug 25, 2025

    • treehouse-diff-expr-proj

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • os_kaplan_meier_plot

      Public
      R
      •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • compendium-expression-matrix

      Public
      Python
      •0•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • CARE

      Public
      Treehouse Comparative Analysis of RNA Expression
      Jupyter Notebook
      •
      Apache License 2.0
      •0•2•4•3•Updated Apr 1, 2025Apr 1, 2025

    • multi-compendia-mapping

      Public
      Python
      •
      MIT License
      •2•0•0•0•Updated Mar 16, 2025Mar 16, 2025

    • HCB_lab_notebook

      Public
      0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

    • 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

    • 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
      •34•0•0•0•Updated Sep 16, 2024Sep 16, 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•13•0•Updated Aug 9, 2023Aug 9, 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
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.