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/YouTubeT...
Link to GEOquery vignette:
https://www.bioconductor.org/packages...
Understanding joins in dplyr: https://statisticsglobe.com/r-dplyr-j...
Show your support and encouragement by buying me a coffee:
https://www.buymeacoffee.com/bioinfor...
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://bioinformagician.org/
Github: https://github.com/kpatel427
Email: [email protected]
#bioinformagician #bioinformatics #genomics #beginners #tutorial #howto #omics #research #biology #ncbi #GEO #rnaseq #ngs
#R #dplyr #tidyverse #GEOquery #data #wrangling #genomics
