Colin Diesh cmdcolin

Linkage Disequilibrium Calculation

This is complete taken from Ryan D on biostar: http://www.biostars.org/p/2909/#16419

It takes a region in a format like "chr2:1234-3456". If an rs number is specified after the region, it will output the R^2 for every SNP in that region with the requested SNP; otherwise, it is all-vs-all.

Frontend Development

Attention: the list was moved to

https://github.com/dypsilon/frontend-dev-bookmarks

This page is not maintained anymore, please update your bookmarks.

Bioconductor Shiny Example #4

Example Shiny App showing an example of being embedded in a larger, non-Shiny workflow.

This is an example Shiny app featuring some basic analysis of Ovarian Cancer gene expression data collected on the Affymetrix U133A platform. We filter the available genes and samples down to a much smaller matrix to make reproducibility simpler for a broader audience. The R code involved in sampling the data is available in this Gist as an R-Markdown file, and the sampled data are available in this Gist as Rds files.

To run the application, install shiny (install.packages("shiny")) then run the following command:

library(shiny)

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

	#!/bin/bash

	while :; do
	stats=$(passenger-memory-stats \| grep Rack)
	if [ "$stats" != "" ]; then
	echo $stats
	echo $stats \| egrep --color=always 'MB ([12][0-9]\|[3-9])..\.. MB'
	pid=$(echo $stats \| egrep 'MB ([12][0-9]\|[3-9])..\.. MB' \| awk '{ print $1 }')
	if [ "$pid" != "" ]; then
	ps aux \| grep $pid

	# 0 is too far from ` ;)
	set -g base-index 1

	# Automatically set window title
	set-window-option -g automatic-rename on
	set-option -g set-titles on

	#set -g default-terminal screen-256color
	set -g status-keys vi
	set -g history-limit 10000

	var fs = require('fs');
	var lame = require('lame');
	var Speaker = require('speaker');

	fs.createReadStream(process.argv[2])
	.pipe(new lame.Decoder())
	.on('format', function (format) {
	this.pipe(new Speaker(format));
	});

	import java.awt.Insets
	import groovy.xml.StreamingMarkupBuilder
	import groovy.transform.*

	class Biostar77288 {
	private int ALN_WIDTH = 1000

	private Map<String,Seq> sequences = [:].withDefault { new Seq( name:it ) }

	private int maxLength = 0

	<html>
	<head>
	<script type="text/javascript">
	//<![CDATA[

	/* from R code https://github.com/genome-vendor/r-bioc-biostrings/blob/master/src/match_PWM.c */

	function compute_pwm_score(pwm, S,offset)
	{
	var score=0.0;

	# From http://garmoncheg.blogspot.com/2012/06/pretty-git-log.html
	git config --global alias.lg "log --color --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)<%an>%Creset' --abbrev-commit --"