Code for Cell-type-specific alternative splicing in the cerebral cortex of a Schinzel-Giedion Syndrome patient variant mouse model

Initial release of "Code for Cell-type-specific alternative splicing in the cerebral cortex of a Schinzel-Giedion Syndrome patient variant mouse model"

starsolo_conda/

The following bash scripts are for running STARsolo on the raw fastq files. These scripts are not required to run if you download processed data from zenodo.

01_build_STAR_genome.sh - The purpose of this script is to build a genome to run STAR.
02_run_STARsolo.sh - The purpose of this script is to run STARsolo with custom filtering parameters to quantify gene and splice junction expression.

seurat/

The following scripts are for processing and filtering the gene expression data.

01_import_filter_data.Rmd - The purpose of this script is to import and filter data using seurat. It is dependent on running the scripts in STARsolo_conda or downloading the data to start. Please use docker image setbp1_alternative_splicing:1.0.4.
02_annotate_cell_types.Rmd - The purpose of this script is to annotate cell types using seurat. It is dependent on seurat script 01. Please use docker image setbp1_alternative_splicing:1.0.4.
functions.R - The purpose of this script is to provide function scripts necessary for analysis.
generate_cellcycle_lists.R

marvel/

The following scripts are for formatting, importing, and analyzing splice junction and expression data using the MARVEL package.

01_format_MARVEL_data.Rmd - The purpose of this script is to format expression data from seurat and SJ outputs from STARsolo for MARVEL. It is dependent on running the seurat scripts 01 and 02. Please use docker image setbp1_alternative_splicing:1.0.5.
02_MARVEL_differential_analysis.Rmd - The purpose of this script is to run differential analysis with MARVEL. It is dependent on running all seurat scripts, and marvel script 01. Please use docker image setbp1_alternative_splicing:1.0.5.
03_analyze_de_genes.Rmd - The purpose of this script is to analyze differential analysis results MARVEL. It is dependent on running all seurat scripts, and marvel scripts 01 and 02. Please use docker image setbp1_alternative_splicing:1.0.6, since you need ComplexHeatmap so make the UpSet plots.
04_calc_sj_usage.Rmd - The purpose of this script is to calculate splice junction usage for each cell type for each splice junction. The data is too sparse to calculate splice junction usage for single cells. It is dependent on running all seurat scripts, and marvel scripts 01 through 03. Please use docker image setbp1_alternative_splicing:1.0.6.
05_cell_specific_sj_expr.Rmd - The purpose of this script is to quantify the splice junction expression across cell types, both per cell and aggregated for each cell type. It creates a new supplemental table that is referred to in the manuscript. It is dependent on running all seurat scripts, and marvel scripts 01 through 04. Please use docker image setbp1_alternative_splicing:1.1.0.
functions.R - The purpose of this script is to provide function scripts necessary for analysis.

deseq2/

The following scripts are for running a pseudobulk differential gene expression analysis

01_pseudobulk_analysis.Rmd - The purpose of this script is to run a pseudobulk gene expression analysis using the cell type data from seurat. It is dependent on seurat scripts 01 and 02. It should be run in docker 1.0.8.
functions.R - The purpose of this script is to provide function scripts necessary for analysis.
Figures

The following scripts are for creating finalized figures for the manuscript

figure_2.Rmd - The purpose of this script is to create a finalized version of figure 2. It is dependent on Marvel scripts 01 through 06. Run in docker 1.0.9.
figure_3-4.Rmd - The purpose of this script is to make and complete figures 3 and 4. Figure 3 has an upset plot of all alternatively spliced genes, and Figure 4 has functional enrichment analysis of cell-type specific AS genes.
figure_5.Rmd - The point of this figure is to convey the importance of the Son gene and also add an additional panel to show where the splice junctions lit on transcript structures.
functions.R - The purpose of this script is to provide function scripts necessary for analysis.
geom_split_violin.R - This is a split violin ggplot function borrowed from jan-glx on stackoverflow
mean_expression_celltype.R - This is a short R script to get average expression for each cell type of a Seurat object
supp_figure_2.Rmd - The purpose of this script is to create a finalized version of supporting information figure 2. It is dependent on Seurat scripts 01 and 02. Run in docker 1.0.6.