PyConAU 2016

Over the weekend I attended PyCon Australia. This was my first time at a purely tech conference and I couldn’t help but compare it to my previous experiences at scientific conferences. DISCLAIMER: Like I said this was my first tech conference and my scientific conference experience is also fairly limited so some of the comments I make might be generalisations that don’t always apply. PyCon started with miniconfs on Friday and continued coding sprints on Monday and Tuesday.

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Recently this paper by Ilicic et al. suggested a method for assessing the quality of individual cells in a single-cell RNA-seq experiment. The basic idea is to extract various biological and technical features from each the reads for each cell, then use PCA with outlier detection or a SVM to classify cells as “high” or “low” quality. There are two pieces of software associated with the paper: cellity, an R package that performs the classification and Celloline, a Python script that performs alignment, summarisation and extraction of alignment statistics such as the number of reads aligned to exons, introns, intergenic regions etc.

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Luke Zappia

Bioinformatician in training

PhD student