BrainSeq Phase II project lead by LIBD for the BrainSeq Consortium
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brainspan
browser
caseControl
caseControl_HIPPO_checks
casecontrolint
correlation
demographics
development
eQTL_GWAS_riskSNPs
eQTL_full
eQTL_full_GTEx
expr_cutoff
gtex
gtex_both
gtex_dlpfc
misc
preprocessed_data
region_specific
supp_tabs
.gitignore
BrainSeq_Phase2_phenotype_data_small_n900.csv
README.md
brainseq_phase2.Rproj

README.md

BrainSeq Phase II analysis

This repository contains analysis code for the BrainSeq Phase II project from the BrainSeq Consortium carried out by researchers at the Lieber Institute for Brain Development.

If you wish to visualize the eQTL results described in this project, please use the LIBD eQTL browser.

License

Attribution-NonCommercial: CC BY-NC

This license lets others remix, tweak, and build upon our work non-commercially as long as they acknowledge our work.

View License Deed | View Legal Code

Citation

If you use anything in this repository please cite the following publication:

Collado-Torres L, Burke EE, Peterson A, Shin JH, Straub RE, Rajpurohit A, Semick SA, Ulrich WS, BrainSeq Consortium, Valencia C, Tao R, Deep-Soboslay A, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE. Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia. bioRxiv, DOI 10.1101/426213. 2018.

Pre-print URL: https://www.biorxiv.org/content/early/2018/09/26/426213.

Files

directory contents
brainspan Code for processing the BrainSpan data.
browser Code for creating the files for the eQTL browser. Contains a detailed README file.
caseControl Initial (un-used) exploratory code for the SCZD case-control analysis. Final code is at the qsva_brain repository.
caseControl_HIPPO_checks Code for checking the SCZD case-control HIPPO results. Final code at qsva_brain repo.
casecontrolint Code for the brain region and SCZD diagnosis status interaction DE analysis.
correlation DLPFC and HIPPO expression correlation analyses.
demographics Code for exploring demographic variables such as RIN.
development Code for the DE analysis across age using a linear spline model.
eQTL_GWAS_riskSNPs eQTL analysis using PGC2 GWAS risk SNPs and neighboring SNPs.
eQTL_full Genome wide eQTL analyses.
eQTL_full_GTEx Replication eQTL analyses using GTEx data.
expr_cutoff Code for filtering the features with low expression values and creating the RSE objects used throughout the project.
gtex Code for processing the HIPPO GTEx data and preparing the genotype data for the eQTL analysis.
gtex_both Code for merging the DLPFC and HIPPO GTEx data.
gtex_dlpfc Code for processing the HIPPO GTEx data.
preprocessed_data Code for processing the RNA-seq reads. Uses the LIBD RNA-seq pipeline developed by EE Burke, L Collado-Torres, and AE Jaffe.
region_specific Code for the DE analyses between HIPPO and DLPFC for prenatal and adult controls.
supp_tabs Code for creating the supplementary tables.
misc Files from early explorations including checking for some sample swaps and quality checks.

LIBD internal:

JHPCE location: /dcl01/lieber/ajaffe/lab/brainseq_phase2