3
$\begingroup$

I am new to R and computational biology. I am trying to look through a published data set to check for gene expression for my own project. I am having trouble finding materials to teach me how to analyze single cell RNA sequencing data on R from the GEO NCBI database.

This is the data that I am trying to access https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138651

I would appreciate any directions or suggestions for tutorials.

Thanks!

Improve this question
$\endgroup$

3 Answers 3

Reset to default
0
$\begingroup$

Install package

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GEOquery")

Use function getGEO to download the files.

expressionSet <- getGEO("GSE138651")
expressionSet <- expressionSet[[1]]

You can then look at the info of the samples:

pData(expressionSet)

And the assay data itself

exprs(expressionSet)
Improve this answer
$\endgroup$
1
  • $\begingroup$ This is useful because of the very specific instructions but I think it would be even more helpful to also include a brief introductory explanation and links to BioConductor and the GEOquery package to provide context for newcomers. $\endgroup$
    – Geraldine_VdAuwera
    May 7, 2020 at 14:51
5
$\begingroup$

The simplest would be using a count matrix (at the end of the link you have shared, section "Supplementary file"). For example GSE138651_Vagal_WholeNodoseSeq_raw.mtx.gz corresponds to "raw" count matrices obtained after mapping and counting the reads. This file, along with the GSE138651_barcodes.tsv.gz and GSE138651_genes.tsv.gz can be used to "read" the data into R; to that end there are many options in the form of packages, Seurat is one of the best documented and hence is beginner-friendly.

Improve this answer
$\endgroup$
3
  • $\begingroup$ Thanks Haci. I am learning Seurat as well. So many things!! I am actually the most interested in the file GSE138651_NGTall_Reads_cap.csv.gz. Do you know if this file type can be "read" into R? $\endgroup$
    – Diana at Duke
    Apr 13, 2020 at 21:28
  • $\begingroup$ Yes, it is a csv file and once again there are many options to read such files into R. read.csv() is one option. Personally, I use fread() of data.table to read in tabular files. $\endgroup$
    – haci
    Apr 13, 2020 at 21:57
  • $\begingroup$ I will try that then. Thank you again! $\endgroup$
    – Diana at Duke
    Apr 14, 2020 at 13:31
0
$\begingroup$

You might want to check out the BioConductor GEOquery package.

Install using 

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GEOquery")

More information on how to use this package and read in data from GEO can be found in the vignette

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.