This page contains information about the software developed by the Bioinformatics Core. For information on initiating a project with the core, please see the Contact page.
The Bioinformatics Core maintains open-source software packages used by researchers worldwide. Some examples include:
Pybedtools makes it possible to use the BEDTools "genome algebra" suite of programs with the Python programming language and offers feature-level access and automatic handling of temporary files. This allows much more complex manipulation of BED-like files than is possible on the command line.
Trackhub streamlines the sharing of genomic data by making it easy to create track hubs for the UCSC Genome Browser.
The Bioconda project maintains thousands of bioinformatics software packaged in a way such that they can be installed on MacOS or Linux into isolated environments. This greatly enhances the reproducibility of computational analyses and eases the installation of complex packages. Bioconda has been adopted by the Galaxy team as their package manager of choice, and packages have been downloaded over 6 million times by researchers worldwide.
A well-tested, best-practices suite of workflows for analyzing high-throughput sequencing data (primarily ChIP-seq and RNA-seq), downloading and managing external published data, and tying everything together into manuscript figures, using the Snakemake workflow language.