Kamil Slowikowski
About Archive

Autocomplete gene names with mygene.info and typeahead.js

I created an example showing how to use mygene.info with typeahead.js. It is possible to autocomplete gene names and retrieve every annotation you can think of (GO, Kegg, Ensembl, position, homologs, etc.).

SNP Proxies

I made a simple web service to list proxies for SNPs in the 1000 Genomes Project. Check out an example of the JSON output. I used it to make an application powered by Highcharts for viewing the r2 linkage disequilibrium plot of any SNP in any population.

Benchmark the binomial probability mass function in Python

It turns out that sympy and scipy have the slowest implementations of the binomial mass function. A pure Python version is just 30 times slower than C in my benchmark. Feel free to copy the code from the IPython notebook and test it for yourself.

Create a quantile-quantile plot with ggplot2

After performing many tests for statistical significance, the next step is to check if any results are more significant than we would expect by random chance. One way to do this is by comparing the distribution of p-values from our tests to the uniform distribution with a quantile-quantile (QQ) plot. Here’s a function to create such a plot with ggplot2.

How to ssh to a remote server without typing your password

Here are a few tips to use ssh more effectively. Login to your server using public key encryption instead of typing a password. Use the ~/.ssh/config file to create short and memorable aliases for your servers. Also, use aliases to connect through a login server into a work server.

Count the number of coding base pairs in each Gencode gene

Use Python to count the coding base pairs in each Gencode gene. Here, the count is reported by gene rather than by transcript, so overlapping exons from multiple transcripts are merged before counting the base pairs.