stephenturner

Gene log2FoldChange pvalue padj
DOK6 0.51 1.861e-08 0.0003053
TBX5 -2.129 5.655e-08 0.0004191
SLC32A1 0.9003 7.664e-08 0.0004191
IFITM1 -1.687 3.735e-06 0.006809
NUP93 0.3659 3.373e-06 0.006809
EMILIN2 1.534 2.976e-06 0.006809

stephenturner

Core Director Meeting: Teaching Materials & Social Media

June 19, 2014

Teaching materials

Workshops

• Galaxy CME Class 10/9/2012 (filled registration)
• Galaxy CME Class 3/5/2013 (filled registration)

stephenturner

# Basic work flows: from SYMBOL to gene model and sequence
# Orig from http://master.bioconductor.org/help/course-materials/2014/ISMB2014/brca1.R

library(org.Hs.eg.db)
eid <- select(org.Hs.eg.db, "BRCA1", "ENTREZID", "SYMBOL")[["ENTREZID"]]

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
txid <- select(txdb, eid, "TXNAME", "GENEID")[["TXNAME"]]
cds <- cdsBy(txdb, by="tx", use.names=TRUE)

stephenturner

Installing poretools without root permission

I needed to install poretools, but the setup instructions assume you have sudo priviliges. After combing through 879868070879 posts on stack overflow, the R-help mailing list, serverfault, etc., I finally arrived at solution using the nuclear option. There may be a better way, but this worked for me.

R

First, nuke and rebuild your own R from source. First, remove your existing installation (as usual, rm -rf with caution...)

rm -rf ~/R

stephenturner

---
title: "Untitled"
author: "Stephen Turner"
date: "September 4, 2014"
output: 
  html_document: 
    keep_md: true
---

This is markdown text.

stephenturner

#######################################################################
#
# import-beadstudio.R
# Stephen Turner, December 2014
#
# Ask the core to export text file data with the info below.
# Assumes control probe file has for each sample:
# ProbeID, AVG_Signal, BEAD_STDERR, Avg_NBEADS, Detection Pval.
# Assumes sample probe file has for each sample:
# ProbeID, Symbol, AVG_Signal, BEAD_STDERR, Avg_NBEADS, Detection Pval

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# RNA-seq: differential gene expression analysis

*[back to course contents](..)*

This is an introduction to RNAseq analysis involving reading in count data from an RNAseq experiment, exploring the data using base R functions and then analysis with the DESeq2 package.

## Install and load packages

First, we'll need to install some add-on packages. Most generic R packages are hosted on the Comprehensive R Archive Network (CRAN, <http://cran.us.r-project.org/>). To install one of these packages, you would use `install.packages("packagename")`. You only need to install a package once, then load it each time using `library(packagename)`. Let's install the **gplots** and **calibrate** packages.

stephenturner

# Generate dataset with 5,000,000 rows, and some random numbers from normal,
# uniform, and cauchy distributions. Write out to file (warning, ~330MB)
n <- 5000000
d <- data.frame(a=1:n, b=rnorm(n), c=runif(n), d=rcauchy(n))
write.table(d, file="test.txt")

# Import the regular way with read.table
system.time(in1 <- read.table("test.txt"))

## Crikey!

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# Get some basic software that you'll need. Edit the first line below. Then update all software and system.
sudo apt-get -y install gcc make vim git
sudo apt-get -y update
sudo apt-get -y upgrade
sudo reboot

## Not necessary, but installing guest additions will allow you to go fullscreen and share files with the host.
# First you'll need the linux headers for your distribution
sudo apt-get -y install linux-headers-generic linux-headers-$(uname -r)
# In Vbox "insert" the guest additions CD, and then cd to /media/user/disc

stephenturner

[include]
	# For user/credentials/token/etc
	path = ~/.gitconfig.local
[core]
	editor = vim
	excludesfile = ~/.gitignore
[color]
	branch = auto
	diff = auto
	status = auto