Analysis of H M project
I have all the scripts I used for integrating HUMAN and mouse tissues
Creating_seurat_startout_objects.Rmd This script creates the startout Human and mouse objects we use for plotting and integration Integration_testing.Rmd This script shows the integration between human and mouse objects Comparisons_between_integration_anal.Rmd This script shows that comparison in metrics between the different forms of integration Diff_accessibility_analysis.Rmd This script identifies the shared, and species specific sites, and looks at the conservation metrics in them Testing_annotated_and_unknown_cells.Rmd Script that was used to annotate previously unannotated and misannotated cells Fibroblast_analyses.Rmd Script used to identify fibroblast subpopulations Per_tissue_dist.Rmd Script used to compare cosine similarity between tissues GO_analysis.Rmd Script used for Gene ontology analysis CCAN_analyses.Rmd Script used for Cis-coaccessibility analysis Replicate_data_analysis.Rmd Analysis of replicate Pneumocyte data Fetal_data_analysis.Rmd Analysis of human fetal data. GWAS_finemapping_res_analysis.Rmd Downstream analysis of Finemapping results GWAS_downstream_analysis.Rmd Hypergeom test analysis and LDSC output analysis