Thomas Yu

Login: thomasyu888

Company: null

Location: null

Bio: null

Blog:

Blog:

Repositories

AACR_Dend

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ansible-galaxy-extras

Ansible roles to configure assorted compontents for an Ubuntu VM or container configured with https://github.com/galaxyproject/ansible-galaxy with production services including nginx, uwsgi, supervisor, protftp, and slurm.

AvonMBCShiny

Shiny Application for MBC

bash_profile

A .bash_profile for your convenience.

bds-files

Supplementary files for my book, "Bioinformatics Data Skills"

beatAMLFacet

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bedtools-protocols

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cbioportal-pipelines

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COCOA-Upload

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common-workflow-language

Repository for CWL Specifications

d3heatmap

A D3.js-based heatmap htmlwidget for R

dalliance

Interactive web-based genome browser.

dermalNF

Code designed to annotate and process CTF-funded dermal NF samples. All available data and key analysis steps uploaded to http://www.synapse.org/dermalNF

dm-docker

Base and example Docker images for the Digital Mammography DREAM Challenge

dm-python-example

This is an example of a DM Challenge submission in Python.

DREAM_DM_starter_code

Some starter code for training/testing some basic CNN models given our data.

dreamtools

Code sharing related to DREAM challenges

Genie

For analyzing data in www.synapse.org/genie

Genome_Browser_conf

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Heatmap-D3

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Helpful-Code

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htmlwidgets

HTML Widgets for R

igv.js

Lightweight html5 version of the Integrative Genomics Viewer

Interactive-bioPlots

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Interactive-Heatmap

d3 heatmap

jbrowse

A modern genome browser built with JavaScript and HTML5.

JSONStream

rawStream.pipe(JSONStream.parse()).pipe(streamOfObjects)

mindboggle

Automated anatomical brain label/shape analysis software (+ website)

nbviewer

Nbconvert as a webservice (rendering ipynb to static HTML)

NTAP

This repository contains various analyses performed for the Neurofibromatosis Therapeutics Acceleration Program (NTAP).

PCBC_DataExplorer_ShinyApp

Interactive DataVis for PCBC expression data

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

planemo-machine

A packer.io configuration for building out Galaxy (http://galaxyproject.org/) tool development environments.

pnfCellLines

This repository focuses on the NTAP-funded analysis regarding plexiform neurofibroma cell lines.

projectMonitoring

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RAKE

A python implementation of the Rapid Automatic Keyword Extraction

rCharts

Interactive JS Charts from R

seqtools

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shiny-js-examples

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SMC-Het-Challenge

Development of the automated scoring system for the SMC-Het Challenge

SMC-RNA-Examples

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synapseAnnotations

Sage Bionetworks derived standards for annotating content in Synapse.

SynapseChallengeTemplates

A collection of templates for use by those writing Synapse challenge scoring applications. The aim is to provide executable examples in various languages (Python, R, Java).

synapseclient

An R package providing programmatic access to Synapse

synapseDocs

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synapsePythonClient

Programmatic interface to Synapse services for Python

synapseRAUtils

Scripts to automate simple/basic research associate tasks

test

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test_CWL

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Trial

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vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

vcf-validator

Validator for Variant Call Format (VCF) files, implemented using C++11

Commits To