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).
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")