This repo documents the data analysis pipeline in reproducible R markdown files for Multi-omics AD PhD skin tape project, submitted as Hu, T et al. Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq . Int. J. Mol. Sci. 2022, 23 (11), 6140
Data is deposited on GEO under the accession GSE199046.
| Rmd | description |
|---|---|
| 01-mapping.Rmd | BRB-seq data mapping |
| 02-dataQCcuration.Rmd | Data QC, curation and explorative analysis (RNA yield, heatmap, PCA, etc) |
| 03-benchmark(LSvsNL).Rmd | Benchmark different count transformation and differential expression testing methods (LS vs Nl) |
| 04-benchmark(LSvsHC_NLvsHC).Rmd | Benchmark ... (LS vs HC, NL vs HC) |
| 05-AD_signature.Rmd | Generate and visualize AD signatures |
| 06-BiopsyvsTape.Rmd | Comparison between full-thickness biopsy and tape stripped skin samples |
| 07-data_submission_GEO.Rmd | Submitting data to GEO |
| 08-benchmark_table_Rpubs.Rmd | Submitting benchmark table to Rpubs |