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    47 repositories

    • mend_qc

      Public
      Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file
      sambambamendrseqcsamblasterdocker
      R
      •
      MIT License
      •0•4•1•1•Updated Dec 13, 2024Dec 13, 2024

    • 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

    • shell-novice2

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Apr 4, 2023Apr 4, 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

    • shell-novice

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Apr 2, 2021Apr 2, 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

    • 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

    • OpenPBTA-analysis

      Public
      The analysis repository for the Open Pediatric Brain Tumor Atlas Project
      HTML
      •
      Other
      •73•0•0•0•Updated Feb 20, 2020Feb 20, 2020