Located in JHPCE at /dcl01/lieber/ajaffe/Amanda/BrainRNACompartments

This repository contains the code used in the analyses in the following citation:

Price, AJ, Hwang, T, Tao, R, Burke, EE, Rajpurohit, A, Shin, JH, Hyde, TM, Kleinman, JE, Jaffe, AE, & Weinberger, DR (2019). “Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation.” bioRxiv, DOI 10.1101/567966.

Pre-print URL: https://www.biorxiv.org/content/10.1101/567966v1.

If you use anything from this repository please cite the above.

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.

Annotation of the included files:

Directory	Description
QC_section	code for processing and cleaning data
RNA_binding_proteins	includes code for calculating enrichment of RNA binding protein motifs and free energy of 3'UTRs in gene sets regulated by fraction
RNA_editing	includes code for identifying and exploring RNA editing sites
RNA_localization_and_age	code for linear regression by fraction and age, exploration of significantly differentially expressed genes
characterize_fractioned_transcriptome	code for exploratory analysis of gene expression differences between fractions, including PCA
disease	code for calculating the enrichment of fraction- and age-associated genes and gene features with disease-associated gene sets
intron_retention	includes code to analyze splicing patterns and intron retention more specifically
other_datasets	includes code used to process and explore publicly available datasets, including the ENCODE fractioned RNA-seq samples
README.md	README file for the github repository
SampleIDs.txt	a list of the sample IDs