Pinned Repositories
b2f_docker
CARE
Treehouse Comparative Analysis of RNA Expression
dgidb
Extract drug gene data from a specific dgidb postgres version for version control
epinano_support
fusion-for-core
UCSC Treehouse Gene Fusion Analysis Pipeline
hub
Tooling to spin up and manage jupyter, nbviewer, xena for tertiary analyis
mend_qc
Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file
pipelines
Makefiles to run dockerized pipelines used in Treehouse on a single sample
shell-novice
xenahub
Stand-alone Dockerized Xena Hub
UCSC Treehouse Childhood Cancer Initiative's Repositories
UCSC-Treehouse/mend_qc
Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file
UCSC-Treehouse/pipelines
Makefiles to run dockerized pipelines used in Treehouse on a single sample
UCSC-Treehouse/CARE
Treehouse Comparative Analysis of RNA Expression
UCSC-Treehouse/fusion-for-core
UCSC Treehouse Gene Fusion Analysis Pipeline
UCSC-Treehouse/dngds-pipelines
DNA Nanopore Genetic Disease Study
UCSC-Treehouse/epinano_support
UCSC-Treehouse/gene_expression_outlier_accuracy
UCSC-Treehouse/shell-novice
UCSC-Treehouse/TUBI-2023
UCSC-Treehouse/TUBI-Manuscript-1
UCSC-Treehouse/xenahub
Stand-alone Dockerized Xena Hub
UCSC-Treehouse/archive
Scripts facilitating the Treehouse storage management
UCSC-Treehouse/brca-exchange
Overall management and deployment of the BRCA Exchange web portal and pipeline scripts
UCSC-Treehouse/ccdi-federation-api
UCSC-Treehouse/compendium-expression-matrix
UCSC-Treehouse/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"
UCSC-Treehouse/hbtest_OpenPBTA-manuscript
The manuscript repository for the Open Pediatric Brain Tumor Atlas Project
UCSC-Treehouse/hexmap-data
compute server for hexmap
UCSC-Treehouse/hexmap-view
UCSC-Treehouse/indwell-bullfrog
UCSC-Treehouse/MEND_qc_survey
UCSC-Treehouse/mini-var-call
Calls and annotates a small curated list of variants from a sorted bam file
UCSC-Treehouse/no-toil-rnaseq
UCSC-Treehouse/OpenPBTA-manuscript
The manuscript repository for the Open Pediatric Brain Tumor Atlas Project
UCSC-Treehouse/protect
UCSC-Treehouse/receiving
As simple as possible, but no simpler, browser upload to S3
UCSC-Treehouse/shell-novice2
UCSC-Treehouse/transcript2genome_coords
UCSC-Treehouse/TUBI-Manuscript
UCSC-Treehouse/TumorMap_Cluster_Analysis
Code for analyzing how samples clusters in the Treehouse TumorMap