Ryan Dale

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

gffutils. GFF and GTF file manipulation and interconversion

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

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

matplotlibrc. some example matplotlibrc files, and a script display their effects

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

dotfiles. dotfiles, batteries included

pipeline-example. example ruffus pipeline

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

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

biomartpy. Simple interface to BioMart (Python -> rpy2 -> R/BioConductor's biomaRt)

ucscsession. Python package for managing sessions in the UCSC Genome Browser.

blender-for-3d-printing. Material for introductory course on using Blender for 3D printing

GFFutils_old. NOTE: see new version at https://github.com/daler/gffutils.

rdbio-scripts. Unorganized collection of bioinformatics scripts and utilities

encode-dataframe. Convert UCSC's ENCODE metadata into pandas DataFrames

enhancer-snakemake-demo. Demos a Snakemake workflow to classify enhancer regions based on publicly available chromatin marks.

gdc. Genomic Dataset Constructor: create example BED, GFF, SAM, FASTQ files from "ASCII art" definitions

genomicfeatures. Python

ontologization. Wrapper for Ontologizer gene ontology analysis tool, with manipulation and display of downstream results

metaseq-biotrac56. Materials for the metaseq presentation at NIH FAES Bio-Trac 56 (http://www.biotrac.com/pages/Tracs/Trac56.html)

seqprint. pretty-print genomic sequences

deseq-browser. View DESeq results in a web browser, with filtering and searching

shiny-fet. Shiny app for visualizing the results of a Fisher's exact test

feature-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 samples

metaseq-example-data. Example data for metaseq

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

entabled. Convert text data files to a browser-viewable version that can be searched, filtered, and sorted

sphinxleash. Lightweight framework for programatically generating Sphinx docs.

docker-rw2019. Materials for docker demonstration for Spring 2019 Reproducibility Workshop

dotfiles-ansible. set up dotfiles on a fresh ubuntu host

marginalhists. Scatterplots with marginal histograms using matplotlib

hubward-studies. Config files for running hubward on published data sets.

build-test. sandbox for bioconda-utils

bedtools. A flexible suite of utilities for genome arithmetic. That is, set theory on genomic features.

trackhub-demo. Python