Mike L. Smith

I’m a bioinformatician working at EMBL Heidelberg as part of the German Network for Bioinformatics Infrastructure (de.NBI).

Welcome

Exploring performance when extracting subsets from HDF5

One of the cool features about the HDF5 file format is the ability to read subsets of the data without (necessarily) having to read the entire file, keeping ...

Parallel processing with R and HDF5

I just got back from a great week at the CZI meeting/workshop/hackathon to mark the start of the ‘Collaborative Computational Tools for the Human Cell Atlas’...

10X single-cell data & HDF5Array performance

Earlier this year 10X Genomics released a single-cell RNA-sequencing dataset containing data from 1.3 million mouse brain cells. The blog post accompanying t...

Default behaviour of `download.file()` on Windows

I recently responded to this post on the Bioconductor forum regarding a problem with reading a HDF5 file using the rhdf5 package. I was initially unable to ...

Using your own version of `libxml2` in R

My previous post here discussed how to build recent versions of R on an old machine that has outdated system libraries. Similarly, sometimes you can get the...