stephenturner

<script language="JavaScript">
$(function() {
  /* Lets the user click on the images to view them in full resolution. */
  $("div.figure img").wrap(function() {
    var link = $('<a/>');
    link.attr('href', $(this).attr('src'));
    link.attr('title', $(this).attr('alt'));
    link.attr('target', '_blank');
    return link;
  });

stephenturner

## devtools::install_github("stephenturner/msigdf")
library(msigdf)
library(dplyr)
library(clusterProfiler)

c2 <- msigdf.human %>% 
    filter(collection == "c2") %>% select(geneset, entrez) %>% as.data.frame

data(geneList)
de <- names(geneList)[1:100]

stephenturner

#!/usr/bin/env bash

# Configuration
remote_target=master
destination=_site

get-working-branch() {
    git status | head -n 1 | awk '{ print $NF }'
}

stephenturner

Deploying a subfolder to GitHub Pages

Sometimes you want to have a subdirectory on the master branch be the root directory of a repository’s gh-pages branch. This is useful for things like sites developed with Yeoman, or if you have a Jekyll site contained in the master branch alongside the rest of your code.

For the sake of this example, let’s pretend the subfolder containing your site is named dist.

Step 1

Remove the dist directory from the project’s .gitignore file (it’s ignored by default by Yeoman).

stephenturner

idat2lumibatch <- function(filenames) {
  # filenames is a character vector of iDAT filenames
  require(illuminaio)
  require(lumi)
  idatlist = lapply(filenames,readIDAT)
  exprs = sapply(idatlist,function(x) {
    return(x$Quants$MeanBinData)})
  se.exprs = sapply(idatlist,function(x) {
    return(x$Quants$DevBinData/sqrt(x$Quants$NumGoodBeadsBinData))})
  beadNum = sapply(idatlist,function(x) {

stephenturner

'''
@author Michael J Bommarito II
@date Feb 26, 2011
@license Simplified BSD, (C) 2011.

This script demonstrates how to use Python to archive historical tweets.
'''

import codecs
import csv

stephenturner

##########################################
# Step 0. setup a list of sample names.  
# Assume that each of your gzipped
# FASTQ files is named as follows:
# sample1.1.fq.gz
# sample1.2.fq.gz
# sample2.1.fq.gz
# sample2.2.fq.gz
# ...
# sampleN.1.fq.gz

stephenturner

##This script get an input file for color-KEGG-pathways
##https://github.com/ajmazurie/color-KEGG-pathways/
##Based from SPIA results at these gists 
##https://gist.github.com/1945349
##https://gist.github.com/1950232

#Load a library needed for text manipulation
#for install run 
#install.packages("stringr")
library("stringr")