UCSC Treehouse Childhood Cancer Initiative

Pinned Repositories

b2f_docker
Language:C++20
CARE
Treehouse Comparative Analysis of RNA Expression
Language:Jupyter Notebook2 2 20
dgidb
Extract drug gene data from a specific dgidb postgres version for version control
Language:Makefile0 3 00
epinano_support
Language:Dockerfile00
fusion-for-core
UCSC Treehouse Gene Fusion Analysis Pipeline
Language:Python1 3 69
hub
Tooling to spin up and manage jupyter, nbviewer, xena for tertiary analyis
Language:Python11
mend_qc
Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file
Language:R4 2 60
pipelines
Makefiles to run dockerized pipelines used in Treehouse on a single sample
Language:Makefile3 2 236
shell-novice
Language:HTML0 2 00
xenahub
Stand-alone Dockerized Xena Hub
Language:Dockerfile0 1 13

UCSC Treehouse Childhood Cancer Initiative's Repositories

UCSC-Treehouse/mend_qc
Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file
Language:R4 2 60
UCSC-Treehouse/pipelines
Makefiles to run dockerized pipelines used in Treehouse on a single sample
Language:Makefile3 2 236
UCSC-Treehouse/CARE
Treehouse Comparative Analysis of RNA Expression
Language:Jupyter Notebook2 2 20
UCSC-Treehouse/fusion-for-core
UCSC Treehouse Gene Fusion Analysis Pipeline
Language:Python1 3 69
UCSC-Treehouse/dngds-pipelines
DNA Nanopore Genetic Disease Study
Language:Makefile0 1 42
UCSC-Treehouse/epinano_support
Language:Dockerfile00
UCSC-Treehouse/gene_expression_outlier_accuracy
Language:HTML00
UCSC-Treehouse/shell-novice
Language:HTML0 2 00
UCSC-Treehouse/TUBI-2023
Language:HTML00
UCSC-Treehouse/TUBI-Manuscript-1
Language:HTML00
UCSC-Treehouse/xenahub
Stand-alone Dockerized Xena Hub
Language:Dockerfile0 1 13
UCSC-Treehouse/archive
Scripts facilitating the Treehouse storage management
Language:Jupyter Notebook2 0
UCSC-Treehouse/brca-exchange
Overall management and deployment of the BRCA Exchange web portal and pipeline scripts
Language:Python
UCSC-Treehouse/ccdi-federation-api
UCSC-Treehouse/compendium-expression-matrix
Language:Python
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
Language:HTML
UCSC-Treehouse/hexmap-data
compute server for hexmap
Language:Python
UCSC-Treehouse/hexmap-view
Language:JavaScript
UCSC-Treehouse/indwell-bullfrog
2 0
UCSC-Treehouse/MEND_qc_survey
Language:HTML3 5
UCSC-Treehouse/mini-var-call
Calls and annotates a small curated list of variants from a sorted bam file
Language:Python3 1
UCSC-Treehouse/no-toil-rnaseq
Language:Shell1 0
UCSC-Treehouse/OpenPBTA-manuscript
The manuscript repository for the Open Pediatric Brain Tumor Atlas Project
Language:HTML1 0
UCSC-Treehouse/protect
UCSC-Treehouse/receiving
As simple as possible, but no simpler, browser upload to S3
Language:JavaScript2 01
UCSC-Treehouse/shell-novice2
Language:HTML
UCSC-Treehouse/transcript2genome_coords
UCSC-Treehouse/TUBI-Manuscript
UCSC-Treehouse/TumorMap_Cluster_Analysis
Code for analyzing how samples clusters in the Treehouse TumorMap
2 0