Annotating variants with a custom file

The Variant Effect Predictor (VEP) tool can be used for annotating variants with respect to custom annotation sources. This is useful if gene models of interest are not represented in the Ensembl or RefSeq databases. To get started, first install VEP since it takes some time.

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Getting started with HISAT, StringTie, and Ballgown

A popular toolset used for analysing RNA-seq data is the tuxedo suite, which consists of TopHat and Cufflinks. The suite provided a start to finish pipeline that allowed users to map reads, assemble transcripts, and perform differential expression analyses. A newer "tuxedo suite" has been developed and is made up of three tools: HISAT, StringTie,...

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7th Anniversary

I reached a million views on 2017 September 27th. Near the start of September, I had wondered if I would reach a million before my 7th anniversary, which is today. I used the traffic to this site to predict when I would hit the mark. Not the best fit. Use only 2017 data to predict....

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Getting started with Monocle

Monocle is an R package developed for analysing single cell gene expression data. Specifically, the package provides functionality for clustering and classifying single cells, conducting differential expression analyses, and constructing and investigating inferred developmental trajectories. The toolkit provides various alternative approaches for each analysis, hence your workflow may differ from the approach I've taken in...

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Rand Index versus the Adjusted Rand Index

I wrote about the Rand Index (RI) and the Adjusted Rand Index (ARI) in the last two posts but how do we interpret the indices and how are they different? The RI is: where and are the number of times a pair of items was clustered concordantly in two different sets. I wrote some code...

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