Meta-analysis_COPD

AIM: Meta-analysis of gene expression experiments on COPD patients

This repository was created to perform a meta-analysis from COPD patients using public data.

It is divided into :

• Tissue/

• Blood/

Each folder has followed this steps, and script can be found in /vignettes:

• 0: Data selection /0-Data-selection.RMD

• 1: Dowload RAW data /1-download_raw-data.RMD

• 2: Normalizing data /2-normalizing-data.RMD

• 3: Curating meta information /3-curatig-data.RMD

• 4: Differential gene expression analysis /4-DE.RMD

• 5: Joing data /5-merge-data.RMD

• 6: Meta-analysis /6-meta-analysis.RMD

• 7: Enrichment-analysis /7-enrichment-analysis.RMD

• 8: Dash-board /8-dashboard.RMD

Additional files that can be found in: https://drive.google.com/drive/folders/1Lw57iquTxWMonUanZPo5G-Yb0QZDDVdP?usp=sharing

All data was downloaded into the computer DNA.lavis.unam.mx and 10.200.0.42(restricted access) and raw data downloaded and normalized (e.i. RMA).

Dashboard

For running the dashboard app you can:

• Access by:

https://anabva.shinyapps.io/8-Meta-analysis-COPD_Dashboard/

• Install locally_

setwd("Dashboard")
rmarkdown::run("8-Meta-analysis_Dashboard.Rmd")