Pig_Bioengineered_Oesophagus_SN_ST

This repository contains the computational environment and code required to reproduce the single-nucleus and spatial transcriptomic analysis in the paper.

The key file here is bioeng_oeso_pipeline.tar, which contains the Docker environment used for the analysis. This can be downloaded, extracted, and the analysis pipeline run using the instuctions in the README. All necessary data is included. Results from the run used for the paper are in a directory results, along with the compiled rmarkdown files. The docker image can be loaded with docker load -i bioeng_oeso_docker_5_d386af43e8f4.tar. The rmarkdown code is also included in this repository.
The Dockerfile and necessary renv.lock file are in the repository to show how to recreate the docker environment. The docker environment was built with build_docker_image.sh

Pre-processing commands run on the computing cluster are shown in preprocessing_commands.sh.

The figures are associated with files as follows:
1f all_sn_before_after_daseq_verdicts_umap.pdf and DimPlot_all_sn_5_clusts.pdf
1g all_sn_module_scores.pdf
1h all_sn_5_clusts_dot_plot_modules.pdf
1i hallmarks_gsea_after_before_all_sn_subset.pdf
1j all_sn_after_vs_before_VolPlot_no_shapes.pdf
1k pathway_marks_vlnplot_all_sn.pdf

3g and 3h sample_celltype_umaps.pdf
3i merged_st_clustered_cell_types_overlay.pdf
3j merged_st_clustered_cell_types_bar_chart_by_pooled_sample.pdf
3k st_samples_connections_chord_diagrams.pdf
3l spatial_connections_similarity_heatmap.pdf

4d st_norm_markers.pdf and vln_plots_Epithelial_extended.pdf

5g st_norm_markers.pdf and vln_plots_Smooth muscle_extended.pdf and vln_plots_Skeletal muscle_extended.pdf

ED3a all_sn_clust_clust_*_all_plots.pdf
ED3b pre_post_by_cluster_barplot.pdf
ED3c heatmap_plus_dots_all_sn_before_after_marker_sets_genes_module_*.pdf
ED3d merged_st_sample_by_cluster_bar_chart_by_pooled_sample.pdf
ED3e inter_cluster_degs_dotplot.pdf

ED8b st_norm_markers.pdf