Computational biology and genomics
Updated 2016 September 15th: I’ve made this into an R package, which is available at my GitHub repository A short post on utilising the OMIM API via some wrapper functions I wrote in R. A wrapper, as explained in the Wikipedia article, is simply a subroutine that calls another subroutine. If you plan on using…
A post on linking OMIM IDs to gene coordinates using biomaRt; this provides a way of representing OMIM IDs on the genome. For those unfamiliar with OMIM, here’s the description from the OMIM FAQ: Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with particular…
Transposons have the ability to “jump” around in genomes and sometimes transposons jump into genomic sites occupied by other repetitive elements; these cases are what I refer to as “composite repetitive elements” for the purpose of this post. While almost all DNA transposons and the majority of retrotransposons have lost the ability to move around…
Here’s a very short post on how to fetch lincRNAs from Ensembl using R and the biomaRt package. For those who are not familiar with biomaRt, you can check out my older post on biomaRt. Firstly, start R and install the biomaRt package from Bioconductor by copying and pasting the code below:
I was recommended to have some sort of cover art on my thesis, so I decided to make my cover using the awesome Gviz package. Below is all the code for how I generated my thesis cover art. Suggestions and comments most welcome!
Updated 2015 April 6th to include the intersect_bed() function in the bedr package. Last year I saw a post on Writing an R package from scratch and I always wanted to follow the tutorial. Yesterday while trying to make some plots using Gviz, I had some BED-like files (not supported by Gviz), which I wanted…
Updated 2015 December 16th: the files for the puzzles can be downloaded from the Amazon cloud Roughly two weeks ago I came across this excellent BEDTools tutorial and saw some puzzles or homework questions at the end of the tutorial; naturally I tweeted about it: Oh this looks like fun; BEDTools puzzles http://t.co/UMowwdPLEf— Dave Tang…
Updated 2015 January 14th I’ll be giving a talk on analysing CAGE data using R in an upcoming workshop held at our institute early next year. I thought it would be a good time to check out slidify, which is an R package that can create HTML slides from R Markdown, since I’m planning on…
Last updated: 2024/12/04 TL;DR As pointed out by Colin, converting a BAM file to CRAM is simply one command: samtools view -T genome/chrX.fa -C -o eg/ERR188273_chrX.cram eg/ERR188273_chrX.bam Of note is that the reference file used to produce the BAM file is required and is used as an argument for the -T option. As for why…
I have written about sequence conservation in vertebrates previously but without much elaboration, hence I’m writing another post on this topic. An assumption of sequence conservation is that regions that show conservation, are under purifying selection, i.e. alleles that decrease the fitness of an organism are removed, and therefore probably do something important. Protein-coding regions…