ucsc-treehouse Goto Github PK

archive

Scripts facilitating the Treehouse storage management

b2f_docker

brca-exchange

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

care

Treehouse Comparative Analysis of RNA Expression

dgidb

Extract drug gene data from a specific dgidb postgres version for version control

dngds-pipelines

DNA Nanopore Genetic Disease Study

docker-pizzly

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"

epinano_support

fusion-for-core

UCSC Treehouse Gene Fusion Analysis Pipeline

gene_expression_outlier_accuracy

hbtest_openpbta-manuscript

The manuscript repository for the Open Pediatric Brain Tumor Atlas Project

hexmap-data

compute server for hexmap

hexmap-view

hub

Tooling to spin up and manage jupyter, nbviewer, xena for tertiary analyis

indwell-bullfrog

jupyterhub

DEPRECATED: See UCSC-Treehouse/hub

jupyterhub-deploy-docker

JupyterHub with docker (for Treehouse students)

mend_qc

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

mend_qc_survey

mini-var-call

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

no-toil-rnaseq

openpbta-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

openpbta-manuscript

The manuscript repository for the Open Pediatric Brain Tumor Atlas Project

pipelines

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

protect

r-intro-2

Introduction to R workshop material, version 2

receiving

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

rna-seq-version-concordance

rna_variant_call

DEPRECATED: See mini-var-call