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UCSC Treehouse Childhood Cancer Initiative (UCSC-Treehouse)

UCSC Treehouse Childhood Cancer Initiative

UCSC-Treehouse

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Home Page:https://treehousegenomics.ucsc.edu/

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UCSC Treehouse Childhood Cancer Initiative's repositories

mend_qc

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

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pipelines

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

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CARE

Treehouse Comparative Analysis of RNA Expression

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fusion-for-core

UCSC Treehouse Gene Fusion Analysis Pipeline

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dngds-pipelines

DNA Nanopore Genetic Disease Study

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epinano_support

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gene_expression_outlier_accuracy

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shell-novice

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TUBI-2023

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TUBI-Manuscript-1

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xenahub

Stand-alone Dockerized Xena Hub

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archive

Scripts facilitating the Treehouse storage management

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brca-exchange

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

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ccdi-federation-api

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compendium-expression-matrix

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EMT-paper

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"

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hbtest_OpenPBTA-manuscript

The manuscript repository for the Open Pediatric Brain Tumor Atlas Project

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hexmap-data

compute server for hexmap

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hexmap-view

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indwell-bullfrog

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MEND_qc_survey

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mini-var-call

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

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no-toil-rnaseq

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OpenPBTA-manuscript

The manuscript repository for the Open Pediatric Brain Tumor Atlas Project

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protect

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receiving

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

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shell-novice2

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transcript2genome_coords

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TUBI-Manuscript

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TumorMap_Cluster_Analysis

Code for analyzing how samples clusters in the Treehouse TumorMap

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