This repo documents the reproducible data analysis pipelines for AD in time and space project.
Check GitHub repo for any update.
View publication in Journal of Investigative Dermatology: Assessment of Spatial and Temporal Variation in the Skin Transcriptome of Atopic Dermatitis by Use of Minimally Invasive Punch Biopsies)
| rmd | description |
|---|---|
| 1-transcriptome-data-cleaning.Rmd | Data cleaning and curation |
| 2-geo-upload.Rmd | Upload data to GEO |
| 3-table1-tableS1.Rmd | Table 1 (Baseline characteristics) and Table S1 (sample metadata, subject metadata) |
| 4-tableS2.Rmd | Table S2 (differential gene expression analysis) |
| 5-figure1.Rmd | Figure 1 (PCA, heatmap, Venn) |
| 6-figure2.Rmd | Figure 2 (Across-study functional enrichment analysis) |
| 7-figure3.Rmd | Figure 3 (Variance partition analysis) |
| 8-figure4.Rmd | Figure 4 (Space variation) |
| 9-figureS1.Rmd | Figure S1 (Transcriptome heatmap, cosine distance) |
| 10-figureS2.Rmd | Figure S2 (Genome regulatory elements) |
| 11-figureS3.Rmd | Figure S3 (Time variation) |
| 12-figureS4.Rmd | Figure S4 (Intraindividual variation) |
| 13-figureS5.Rmd | Figure S5 (Time fluctuation of disease severity) |
| 14-figureS6.Rmd | Figure S6 (Correlation heatmap of IL34, IL37, UGT3A2 and inflammatory biomarkers) |
- RNA-seq data is available at GEO under the accession number GSE193309