Analysis of Age-related Changes in Intercellular Communication from scRNA-seq
- analysis - main folder with final analysis
- src - folder with utility functions
- test - folder to test and benchmark specific parts of codes
- shinyApp - code for the web app
- old_deprecated - code to keep temporarily (will be removed eventually)
Note: it should not be necessary to run analysis 1-4 each time if the data are already stored.
- analysis_1_Seurat_processing.R - verifies the integrity of Seurat files
- controls the content of the files
- checks that QC has been done properly
- produces some statistical information and plots about each dataset/tissue/cell-type
- analysis_2_LRdb_selection.R - compares the 4 LR databases
- summary and Venn diagram
- selection of relevant LR-pairs
- GO enrichment analysis on the LR pairs
- analysis_3_run_scDiffCom.R - does scDiffCom analysis on all datasets
- run in parallel over all tissues (one dataset at a time)
- need to be called each time for each dataset
- analysis_3b_run_diffcom_whole_dataset.R - not functional for now...
- attempt to consider the entire dataset as a single tissue
- not working yet, requires too much memory (even on the server)
- not sure if this is a relevant analysis
- analysis_4_filtering_ora_fpm.Rmd - first downstreamn analysis
- perform filtering
- perform overrepresentation analysis
- perform frequent pattern mining
- we need to discuss the choice of cutoffs
- TODO
- add future downstream analysis (general stats, enrichment, more plots, etc)
Note: each script can be run independently, as long as some data files are stored. Additional files can also be added if more tests are needed.
- test_1_scDiffcom.R - checks that scDiffCom returns correct values
- requires a Seurat file for testing (e.g: "../data_scAgeCom/data_seurat_example.rds")
- shows typical usage of scDiffCom
- checks scores and p-values (from independent functions)
- create plots to compare distributions from permutations
- test_2_compare_to_cpdb.R - check that scDiffCom returns similar values compared to CellPhoneDB
- requires preprocessed CPDB output
- shows (deprecated) usage of run_cpdb_from_seurat
- shows that LR scores are exactly the same between the methods
- shows that LR specificity p-values are similar (up to randomness)
- shows high similarity in classifying significant/non-significant CCIs
- test_3_scDiffCom_parameters - compare scDiffCom results for different methods/parameters
- compares normalization, log-scale and x-sided test
- checks the classification of each CCI for each choice of parameters
- checks the shape of the distributions from the permutation tests
- TODO
- do test with another file, e.g. from Calico
- add more test related to LR_score cutoff
- clarify how test_3 can help us to justify our choice of parameters
- clarify the origin of the strange cases whith very low distribution means