Beast code in Giters

Ryan Dale's repositories

pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

Language:PythonNOASSERTION293 17 287

gffutils

GFF and GTF file manipulation and interconversion

Language:PythonMIT268 14 146

metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data

Language:PythonMIT87 22 37

trackhub

create, manage, and upload track hubs for use in the UCSC genome browser

Language:PythonMIT51 8 20

sphinxdoc-test

experimenting with the best way to push sphinx-generated docs to gh-pages

24 20

hubward

Manage the visualization of large amounts of other people's [often messy] genomics data

Language:PythonBSD-3-Clause18 3 1

dotfiles

dotfiles, batteries included

Language:Shell16 3 6

chromhmm-tools

Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)

Language:Python15 3 4

blender-for-3d-printing

Material for introductory course on using Blender for 3D printing

Language:PythonNOASSERTION10 20

rdbio-scripts

Unorganized collection of bioinformatics scripts and utilities

Language:Python10 3 1

shiny-fet

Shiny app for visualizing the results of a Fisher's exact test

Language:RMIT3 20

chromhmm-enhancers-umel

Identify enhancers. Includes data download, liftover, parallelized workflows, results aggregation, and example output.

Language:PythonMIT2 20

docker-rw2019

Materials for docker demonstration for Spring 2019 Reproducibility Workshop

Language:HTMLMIT2 20

sphinxleash

Lightweight framework for programatically generating Sphinx docs.

Language:PythonMIT2 20

build-test

sandbox for bioconda-utils

Language:Python1 20

hubward-studies

Config files for running hubward on published data sets.

Language:Python1 20

trackhub-demo

Language:Python1 20

2015-09-09-NIH

Language:PythonNOASSERTION020

aerial.nvim

Neovim plugin for a code outline window

Language:LuaMIT000

bioconda-recipes

Conda recipes for the bioconda channel.

Language:Shell020

bioconda-utils

Utilities for building and managing bioconda recipes

Language:PythonMIT020

connect-test

temp repo for testing github status updates

020

docker-dokuwiki

Language:DockerfileGPL-3.0000

erythroid-genes

Documents the construction of mouse erythroid gene lists

Language:HTMLMIT02 1

NIHCloudLabAWS

Documentation and tutorials on using AWS for biomedical research

Language:Jupyter Notebook000

Pharmacogenomics_Prediction_Pipeline_P3

Language:RCC0-1.0020

rsconnect

Publish Shiny Applications, RMarkdown Documents, Jupyter Notebooks, Plumber APIs, and more

Language:R000

vim-python-pep8-indent

A nicer Python indentation style for vim.

Language:Vim ScriptCC0-1.0000

vogt-particle-tracking

Code to reproduce analysis from Vogt et al 2019 Nature Communications

Language:Jupyter NotebookMIT020

zenburn.nvim

Zenburn for the modern age

Language:LuaMIT000