SOFTWARE DEVELOPED BY THE BFG
All of our work has led at various points to generation of new algorithms and software. In order to ensure that our bioinformatics analyses are reproducible and available to fellow researchers, we have adopted a philosophy of open source and work with public software repositories to release it. Much of this work appears as publications in addition to easily downloaded packages, but exists primarily in two forms: as a package on Bioconductor or as an installable, Bioconductor-compatible package on github. The reasons for the latter category are largely that packages often take many months to years to make it through the Bioconductor vetting process, and so we make it available through git for convenience.
What kind of software?
Most of our software and workflows are related to downstream analyses of next-gen sequencing data (NGS). Data are processed in multiple stages; first off the sequencer individual reads are matched to the reference human genome (alignment). Next the aligned reads are mapped relative to genes or other features of interest. For some data (e.g. methylation) there are additional steps. Most of our software concerns the biological questions that are of interest after these other steps have been completed. This includes integration with genetic data (funciSNP, funciVar), chromatin state identification, allelic imbalances, integration with expression data (HiCAGE, ELMER), and identification of potential disruptive sequences (motifBreakR), to name a few.
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