Getting started with GEMINI

After getting started and getting acquainted with DNA sequencing data, it's finally time to explore DNA variation. A tool that makes this easy is GEMINI and this post briefly demonstrates some of its functionality. I have only used GEMINI sparingly and what I know about the tool is gathered mostly from their documentation and tutorials....

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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...

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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...

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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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Repetitive elements in vertebrate genomes

Updated 2015 February 8th to include some scatter plots of genome size versus repeat content. I was writing about the make up of genomes today and was looking up statistics on repetitive elements in vertebrate genomes. While I could find individual papers with repetitive element statistics for a particular genome, I was unable to find...

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Genomic Regions Enrichment of Annotations Tool

The Genomic Regions Enrichment of Annotations Tool (GREAT) is a tool that allows you to find enriched ontological terms in a set of genomic regions. This talk (running time ~1 hour) gives an overview of the tool. In brief, GREAT is an alternative to gene-centric enrichment tools such as DAVID and uses a binomial test...

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Bioconductor annotation packages

The Bioconductor annotation packages are an extensive collection of annotations. For this post I simply illustrate the basics of probing these annotation packages. For the first example I will use the org.Hs.eg.db package, which provides genome wide annotations for the human genome. We can query the package by using the select() function; to find out...

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