Getting started with the OMIM API

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 the OMIM API, first register for your very own API key. After you submit the form you will get an email with the key, along with this message:

The API key will be activated within TWO hours, trying to use it before then will result in a error. It is for your own use, we ask that you do not share it with others.

So if you haven't already registered, stop reading now, and submit the form.

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OMIM IDs to gene coordinates

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 focus on the molecular relationship between genetic variation and phenotypic expression.

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Finding composite repetitive elements

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 in the human genome, transposition events that have occurred in the past are captured within the genome sequence. This post is about finding composite repetitive elements in the human genome based on RepeatMasker annotations.

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How do I fetch lincRNAs from Ensembl?

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:


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