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pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")gffutils
GFF and GTF file manipulation and interconversiontrackhub
create, manage, and upload track hubs for use in the UCSC genome browsermatplotlibrc
some example matplotlibrc files, and a script display their effectssphinxdoc-test
experimenting with the best way to push sphinx-generated docs to gh-pagesdotfiles
dotfiles, batteries includedhubward
Manage the visualization of large amounts of other people's [often messy] genomics datapipeline-example
example ruffus pipelinebiomartpy
Simple interface to BioMart (Python -> rpy2 -> R/BioConductor's biomaRt)chromhmm-tools
Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)ucscsession
Python package for managing sessions in the UCSC Genome Browser.blender-for-3d-printing
Material for introductory course on using Blender for 3D printingrdbio-scripts
Unorganized collection of bioinformatics scripts and utilitiesGFFutils_old
NOTE: see new version at https://github.com/daler/gffutils.encode-dataframe
Convert UCSC's ENCODE metadata into pandas DataFramesenhancer-snakemake-demo
Demos a Snakemake workflow to classify enhancer regions based on publicly available chromatin marks.genomicfeatures
gdc
Genomic Dataset Constructor: create example BED, GFF, SAM, FASTQ files from "ASCII art" definitionsontologization
Wrapper for Ontologizer gene ontology analysis tool, with manipulation and display of downstream resultsseqprint
pretty-print genomic sequencesmetaseq-biotrac56
Materials for the metaseq presentation at NIH FAES Bio-Trac 56 (http://www.biotrac.com/pages/Tracs/Trac56.html)deseq-browser
View DESeq results in a web browser, with filtering and searchingshiny-fet
Shiny app for visualizing the results of a Fisher's exact testmetaseq-example-data
Example data for metaseqchromhmm-enhancers-umel
Identify enhancers. Includes data download, liftover, parallelized workflows, results aggregation, and example output.sphinxleash
Lightweight framework for programatically generating Sphinx docs.docker-rw2019
Materials for docker demonstration for Spring 2019 Reproducibility Workshopfeature-by-reads-matrix
Collection of scripts to create a table of genome features with the number of reads per feature for an arbitrary number of samplesentabled
Convert text data files to a browser-viewable version that can be searched, filtered, and sortedmarginalhists
Scatterplots with marginal histograms using matplotlibtrackhub-demo
build-test
sandbox for bioconda-utilshubward-studies
Config files for running hubward on published data sets.Love Open Source and this site? Check out how you can help us