Computational biology and genomics
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.
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,…
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….
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…
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 $$a$$ and $$b$$ are the number of times a pair of items was clustered concordantly in two different sets. I wrote…
In my last post, I wrote about the Rand index. This post will be on the Adjusted Rand index (ARI), which is the corrected-for-chance version of the Rand index:
I’ve been looking for ways to compare clustering results and through my searching I came across something called the Rand index. In this short post, I explain how this index is calculated.
I have started to work on Arabidopsis thaliana, as I mentioned in my last post. As noted in the Encyclopedia of life: Arabidopsis thaliana is the most widely used model organism in plant biology. Its small genome size, fully sequenced in the year 2000, chromosome number, fast growth cycle (from seed germination to set in…
The Gene Transfer Format (GTF) is a refinement of the General Feature Format (GFF). A GFF file has nine columns: seqname The name of the sequence; must be a chromosome or scaffold. source The program that generated this feature. feature The name of this type of feature, e.g. “CDS”, “start_codon”, “stop_codon”, and “exon” start The…
Updated 2018 April 11th This post follows the Peripheral Blood Mononuclear Cells (PBMCs) tutorial for 2,700 single cells. It was written while I was going through the tutorial and contains my notes. The dataset for this tutorial can be downloaded from the 10X Genomics dataset page but it is also hosted on Amazon (see below)….