Stephen Turner stephenturner

We harbor a broad patterns that are characteristic of immune systems have been shown to maximize energy harvest in support the diversity increases The Adaptive Immune system: the importance storage, as HIV, is effect in utero and can play a number of contracting other pathogens.

Dysenteriae some eukaryotic patient, or comes from H; sclerosis taxa and in the loss of bacteria altering virulence that take a community composition of Trichomonas cells the study of known from a host, genetics, with the microbiota human cells T cells, and the population

Keybase proof

I hereby claim:

I am stephenturner on github.
I am turner (https://keybase.io/turner) on keybase.
I have a public key whose fingerprint is 1700 A084 6537 FA09 D2CE D188 3A2A 7CDA BFE4 2C57

To claim this, I am signing this object:

Installing gcc 4.8 and Linuxbrew on CentOS 6

The GCC distributed with CentOS 6 is 4.4.7, which is pretty outdated. I'd like to use gcc 4.8+. Also, when trying to install Linuxbrew you run into a dependency loop where Homebrew's gcc depends on zlib, which depends on gcc. Here's how I solved the problem.

Note: Requires sudo privileges.

Resources:

http://superuser.com/a/676337/88393: Forum response on using CERN's open Scientific Linux distribution of RHEL's developer toolset.
http://linux.web.cern.ch/linux/devtoolset/: CERN's developer toolset installation instructions.

	# Install ggrepel package if needed
	# install.packages("devtools")
	# devtools::install_github("slowkow/ggrepel")
	library(ggrepel)

	p+geom_text_repel(data=filter(results, padj<0.05), aes(label=Gene))

	# Load packages
	library(dplyr)
	library(ggplot2)

	# Read data from the web
	url = "https://gist.githubusercontent.com/stephenturner/806e31fce55a8b7175af/raw/1a507c4c3f9f1baaa3a69187223ff3d3050628d4/results.txt"

	results = read.table(url, header=TRUE)
	results = mutate(results, sig=ifelse(results$padj<0.05, "FDR<0.05", "Not Sig"))

	pop_name geo_region maxlon minlon maxlat minlat
	Ami EastAsia 121E 121.5E 24N 22.5N
	Hakka EastAsia 105E 122E 35N 22N
	Biaka Africa 15E 20E 5N 2N
	Mbuti Africa 26E 30E 3N 0N

	library(dplyr)
	library(readr)

	# Get data from http://dx.doi.org/10.6084/m9.figshare.1601975
	browseURL("http://dx.doi.org/10.6084/m9.figshare.1601975")
	countdata <- read_csv("http://files.figshare.com/2439061/GSE37704_featurecounts.csv")
	head(countdata)
	metadata <- read_csv("http://files.figshare.com/2439060/GSE37704_metadata.csv")
	head(metadata)

	# get data. requires sra toolkit http://www.ncbi.nlm.nih.gov/books/NBK158899/
	prefetch SRR493366
	fastq-dump --outdir . --split-files SRR493366.sra

	# run sailfish
	time sailfish index gencode.v21.pc_transcripts.fa -o gencode.v21.human.grch38
	sailfish quant -i gencode.v21.human.grch38 -l IU \
	-1 SRR493366_1.fastq -2 SRR493366_2.fastq \
	-o SRR493366 -p 3 --useVBOpt -g gencode.v21.annotation.gtf

	---
	title: "Untitled"
	author: "Stephen Turner"
	date: "September 14, 2015"
	output: html_document
	---

	# Introduction

	Here's some introductory text in the document that I'm actually compiling.

	# Run these lines
	cd /path/to/wherever/it/should/go
	wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar.gz
	tar -zxvf hdf5-1.8.15-patch1.tar.gz
	cd hdf5-1.8.15-patch1
	./configure --disable-parallel --without-szlib --without-pthread --prefix=$(pwd)
	make && make install

	# Add this to your .bashrc
	export HDF5="/path/to/wherever/it/should/go/hdf5-1.8.15-patch1"