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    50 repositories

    • HCB_lab_notebook

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

    • neuromuscular-disease-sample-analysis

      Public
      UCSF Dr. Alex Fay's 15 Undiagnosed Pediatric Neuromuscular Diseases (NMDs). RNA sequencing (ribs deplete) had been conducted. Subsequent analysis include outlier analysis, splicing analysis, and junction usage analysis.
      0•0•0•0•Updated Feb 10, 2025Feb 10, 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

    • mend_qc

      Public
      Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file
      sambambamendrseqcsamblasterdocker
      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
      •
      Apache License 2.0
      •1•0•0•0•Updated Apr 21, 2021Apr 21, 2021

    • MEND_qc_survey

      Public
      HTML
      •
      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