Skip to content

Multi-omics AD PhD project bookdown documenting the reproducible data analysis pipeline

License

Notifications You must be signed in to change notification settings

tuhulab/AD-time-space

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Atopic dermatitis in time and space

This repo documents the reproducible data analysis pipelines for AD in time and space project.

Data analysis pipeline

DOI

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)

Shiny application for data exploration and downloading

Data availability

  • RNA-seq data is available at GEO under the accession number GSE193309

About

Multi-omics AD PhD project bookdown documenting the reproducible data analysis pipeline

Resources

License

Stars

Watchers

Forks

Packages

No packages published