temporal-brain-expression

Scripts to analyze spatio temporal brain expression based on the BrainSpan Developmental Transcriptome data.

BrainSpan Data

Click here to download the RNA-seq data (genes_matrix_csv.zip, 62.2 MB).

For more information, please refer to the BrainSpan Developmental Transcriptome webpage.

Documentation

1. Download the BrainSpan RNA-seq data (same file as referred to above).
2. Enter the correct paths in CONFIG.R. This is needed to load the BrainSpan data and control where the output files will be written.
3. Change to the src/ directory.
4. Run R CMD BATCH read_rnaseq_data.R to load and process the BrainSpan data. The script generates two .RData files with the BrainSpan data (Run time is approx. 15 min.).
5. Perform analysis
6. Run R CMD BATCH graphics_genes_temporal_trajectories.R to produce gene trajectory plots.
7. Run R CMD BATCH statistics_prenatal-vs-postnatal-test.R to compare expression levels in prenatal vs postnatal developmental stages.

Individual scripts contains comments explaining the analysis steps.

System Requirements

• R (version >= 3.1)
• R packages: plyr, dplyr, ggplot2, reshape2 and tools
• 12 GB RAM

The scripts have only been tested on OSX and Linux operation systems.