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db.host=localhost
db.user=hguser
db.password=hguser
db.trackDb=trackDb

central.db=hgcentral
central.host=localhost
central.user=hguser
central.password=hguser
central.domain=

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{
 "metadata": {
  "name": "hw1"
 }, 
 "nbformat": 2, 
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "markdown", 

sjackman

# STAT 540 Seminar 5
# Shaun Jackman
# 2013-01-30

# Brief pause to load the photoRec data and the lattice package
library(lattice)  # if you don't already have this loaded ...
prDat <- read.table("../data/photoRec/GSE4051_data.txt")  # the whole enchilada
str(prDat, max.level = 0)
load("../data/photoRec/GSE4051_design.robj")  # load exp design as 'prDes'
str(prDes)

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# STAT 540 Seminar 6
# Shaun Jackman

# Preliminaries
library(limma)
library(lattice)
prDat <- read.table("../data/photoRec/GSE4051_data.txt")  # the whole enchilada
str(prDat, max.level = 0)
load("../data/photoRec/GSE4051_design.robj")  # load exp design as 'prDes'
str(prDes)

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# STAT 540 Homework 1
# Shaun Jackman
# 2013-02-18

library(lattice)
library(limma)
library(preprocessCore)
library(reshape2)

design <- read.table('gse7191_design.txt')

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# STAT 540 Seminar 7
# Shaun Jackman

library(biomaRt)
library(easyRNASeq)
library(Rsamtools)
library(ShortRead)
library(BSgenome.Dmelanogaster.UCSC.dm3)

# Reading BAM Files

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# STAT 540 Seminar 8
# Shaun Jackman

# edgeR
library(edgeR)
dat <- read.table("../data/bottomly/bottomly_count_table.txt",
	header = TRUE, row.names = 1)
des <- read.table("../data/bottomly/bottomly_phenodata.txt",
	header = TRUE, row.names = 1)
all(rownames(des) == colnames(dat))

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# STAT 540 Seminar 9
# Shaun Jackman

# Data Preparation
library('RColorBrewer')
library('car')
library('lattice')
library('limma')
library('pvclust')
library('xtable')

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#!/usr/bin/make -Rrf
# Parallelize wc by implementing map/reduce in make
# Written by Shaun Jackman.

# Number of chunks
n=4

all: words.wc words.mapreduce.wc

clean: