Computational biology and genomics
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…
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:
If you’ve worked in the genomics field, then you’ve most likely spent some time converting gene identifiers to other gene identifiers or to gene symbols. Some common gene annotation databases include RefSeq, UCSC known genes, Entrez gene and Ensembl genes. In the past, I’ve relied on large tables that provide the lookup between different identifiers,…
In the past I’ve been manually downloading tables of data annoation and parsing them with Perl. I guess it’s time to do things more elegantly. Below is code taken from the biomaRt vignette: Note If you are using Ubuntu and getting a “Cannot find xml2-config” problem while installing XML, a prequisite to biomaRt, try installing…