brentp

sudo apt-get install libtool
git clone git://dnaa.git.sourceforge.net/gitroot/dnaa/dnaa dnaa-git
cd dnaa-git
# bfast required. see above gist
cp -r ../bfast-git ./bfast
# samtools require. see above gist.
cp -r ../samtools-svn/ ./samtools

sh autogen.sh && ./configure && make && sudo make install

brentp

ORG=hg19
USER=brentp

# from: http://nsaunders.wordpress.com/2011/05/18/how-to-create-a-partial-ucsc-genome-mysql-database/

# create database
mysql -u $USER  -e "CREATE DATABASE $ORG";
mkdir -p ucsc-data/$ORG
cd ucsc-data/$ORG
for table in knownGene refGene ensGene kgXref chromInfo cpgIslandExt cytoBand

brentp

# NOTE the /Modules/

./configure --prefix=/vol1/home/brentp/installed/ \
     --with-python-config-dir=/vol1/home/brentp/src/python/Python-2.7.2/Modules/ \
     --enable-pythoninterp=yes --with-features=huge 

ogrisel

Line #      Hits         Time  Per Hit   % Time  Line Contents
==============================================================
   627                                           def expected_mutual_information(contingency, n_samples):
   628                                               """Calculate the expected mutual information for two labelings."""
   629        25           82      3.3      0.0      R, C = contingency.shape
   630        25           53      2.1      0.0      N = n_samples
   631        25         1059     42.4      0.0      a = np.sum(contingency, axis=1, dtype='int')
   632        25          932     37.3      0.0      b = np.sum(contingency, axis=0, dtype='int')
   633        25           58      2.3      0.0      emi = 0
   634      1839         4005      2.2      0.0      for i in range(R):

taoliu

#!/usr/bin/env python

import subprocess
import sys
import os
import time

#time_stamp=time.strftime("%y-%m-%d_%H-%M-%S")
time_stamp=str(time.time())

arq5x

##########################################
# 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

arq5x

Genome arithmetic for data exploration

The goal of today's practical session is to get your hands dirty with bedtools. We will be studying ChiP-seq data from three different cell types. Each cell type was assayed for H3K27ac. Our research goal is to understand and explore the similarities and differences between the ChIP peaks observed in the 3 different cell types.

brentp

library(SNPRelate)
library(FDb.UCSC.snp137common.hg19)
library(hash)

args = commandArgs(TRUE)

vcf.fn = args[1]


gds.fn = paste0(args[1], ".gds")

17twenty

package main
import (
	"./binding"
	"fmt"
)

func main() {
	binding.PrintHello()
	binding.Seed(1)
	fmt.Println(binding.Random())

bsima

For most of the tools on here, if you follow the GitHub repos back to the user that owns the repo, they usually have other cool Clojure tools they build. Just a general observation about the Clojure community.

Learnings

• Clojure home - There's a ton of good stuff here, like the rationale behind the design and explanations of the best features of Clojure.
• Clojure.github.io - The core Clojure documentation. Useful for looking up functions and such.
• Clojuredoc - Community written Clojure documentation and articles
• Clojure Koans - Learn Clojure with Koans
  • When you get stuck, use these YouTube videos to help you.
• 4Clojure - Solve simple problems to stretch your Clojure skills