GabrielHoffman/dream_analysis

Simulation and data analysis code for dream paper

dream: Powerful differential expression analysis for repeated measures designs

dream is available in the Bioconductor package variancePartition ⩾ v1.10.1 for Bioconductor ⩾ v3.7. You may need to install R ⩾ v3.5.

See dream documentation.

Simulations

See code in sims/master_analysis.sh

Data analysis

Data and annotation are stored on Synapse. In order to run these scripts, you will need the Synapse client for R and a Synapse account.

Links point to original publication, public data, html files from current analysis, and text files from differential expression analysis. rmarkdown::render code snippet will regenerate results and html files.

• Timothy Syndrome | paper, data, html, results

rmarkdown::render("src/iPSC_Timothy.Rmd", output_dir='./', intermediates_dir='./')

• Alzheimer's disease | paper, data, html, results

rmarkdown::render("src/AMP_AD.Rmd", output_dir='./', intermediates_dir='./')

• Childhood onset schizophrenia | paper, data, html, results

rmarkdown::render("src/COS.Rmd", output_dir='./', intermediates_dir='./')

• Epigenetic map of the human brain | paper, data, html, results

rmarkdown::render("src/EpiMap.Rmd", output_dir='./', intermediates_dir='./')

Dependencies

Install R dependencies

# Packages used by data analysis code
packages = c(
	'Biobase',
	'GEOquery',
	'GenomicRanges',
	'RcppRoll',
	'biomaRt',
	'data.table',
	'doParallel',
	'edgeR',
	'foreach',
	'genomation',
	'ggplot2',
	'grid',
	'gridExtra',
	'knitr',
	'limma',
	'qvalue',
	'scales',
	'variancePartition')

# Install from Bioconductor or CRAN
# Assumes you've already installed Bioconductor 
# 	http://bioconductor.org/install
BiocManager::install( packages )

# Install synapser developed by Sage Bionetworks
# 	https://r-docs.synapse.org/
install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))