How to manipulate gene expression data from NCBI GEO in R using dplyr | Bioinformatics for beginners

This is a basic hands-on tutorial to manipulate gene expression (RNA-Seq) data from NCBI GEO in #R using the dplyr package.
In this video, I have demonstrated how to read gene expression data in R, retrieve metadata using the GEOquery R package, and perform data manipulation using basic dplyr functions.

Link to code: https://github.com/kpatel427/YouTubeTutorials/blob/main/dataManipulation.R

Link to GEOquery vignette:
https://www.bioconductor.org/packages/devel/bioc/vignettes/GEOquery/inst/doc/GEOquery.html

Understanding joins in dplyr: https://statisticsglobe.com/r-dplyr-join-inner-left-right-full-semi-anti

Chapters:
0:00 Intro
0:48 Requirements
0:55 Set up RStudio for Analysis
5:50 Read data in R
8:31 Get metadata using GEOquery package
13:16 dplyr: select(), rename(), mutate()
20:57 Reshape data: gather()
25:42 Join data: left_join()
28:55 dplyr: filter(), group_by(), summarize(), arrange()


To get in touch:
Website: https://khushbupatel.info/
Github: https://github.com/kpatel427
Email: khushbu_p@hotmail.com

#bioinformagician #bioinformatics #genomics #beginners #tutorial #howto #omics #research #biology #ncbi #GEO #rnaseq #ngs
#R #dplyr #tidyverse #GEOquery #data #wrangling #genomics