The Adjusted Rand index
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:
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.
Getting started with Arabidopsis thaliana genomics
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...
Read GTF file into R
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...
Getting started with Seurat
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). The PBMCs, which are...
Learning about Snakemake
As promised two years ago, here's a short blog post on Snakemake. I have been using Bpipe to manage my workflows/pipelines but Snakemake has been mentioned to me on more than one occasion; in particular: @davetang31 seems useful if testing many diff types of pipelines. snakemake seems a bit more practical if analyzing many samples...
Deleteriousness versus pathogenicity
What's the difference between deleteriousness and pathogenicity? Box 1 from the article "Guidelines for investigating causality of sequence variants in human disease" has the following definitions: