bioinformatics

ATAC-Seq workshop

This workshop introduces ATAC-Seq, quality control approaches, isolating nucleosome compartments, and profile plots and heatmaps.

Statistical Methods in Functional Genomics

In a series of talks and exercises, I cover introduction to R, Bioconductor, genomic ranges, container classes, annotation of genes and regions, ATAC-Seq data analysis, and an introduction to machine learning.

Single cell packages and dependencies in Bioconductor using BiocPkgTools

The Bioconductor package ecosystem continues to grow at an exponential rate (check it–I am right). We have recently completed the BiocPkgtools package that can mine package metadata, build reports, dependencies and can produce interesting plots of package dependencies. I was recently asked about the dependency structure of packages labeled by the package authors (using biocViews) as “SingleCell”. I am posting the code here, just for fun.

Orchestrating a community-developed computational workshop and accompanying training materials

The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for effective instruction and education. A workshop setting, with lectures and guided hands-on tutorials, is a common …

GenomicDataCommons Example: UUID to TCGA and TARGET Barcode Translation

One of the features of the NCI Genomic Data Commons is that everything has a unique identifier in the form of a UUID. However, because many legacy projects and much of the literature do not use UUIDs but instead use TCGA sample barcodes, one simple use case for the GenomicDataCommons package is to map from the UUID for a file or a set of files back to the associated TCGA barcode(s).