README.md

Experimental workflow

Computational workflow

Public release of code for analysis for COS cohort

All code is in R and depends on packages from CRAN and Bioconductor.

Code automatically downloads data from Synapse project.

Data is available from Synapse

Install dependencies

First, install ENSEMBL v70 annotations

R CMD INSTALL library/EnsDb.Hsapiens.v70_0.0.tar.gz

You will need to install additional packages that R requests including the R SynapseClient.

View results pages

Core analysis

Differential expression concordance

Coexpression

CNV analysis

Run Analysis

Run first analysis in R:

rmarkdown::render("analysis_public_release.Rmd")

CNV plots:

rmarkdown::render("CNV.Rmd")

Concordance between this dataset and CommonMind, NIMH HBCC

Note: requires proper to permissions from the CommonMind project:

You must register with Synapse and have permission to read download this data

rmarkdown::render("compare_differential_expression.Rmd")

Coexpression analysis:

rmarkdown::render("run_WGCNA.Rmd")

eQTL enrichment analysis:

# Generate files with run_eQTL_enrichments.R 
# Run analysis with enrichment_analysis.R based on bash code at the end of run_eQTL_enrichments.R