cantin-ortiz / molecular-atlas Goto Github PK

Hello!

Thank you very much for your work.

I have a question. I am now processing the spatial transcriptome data in your article, starting with the fastq file. But I can't find the ‘ids’ file which containing the barcodes and array coordinates. Would it be convenient for you to provide me with the ‘ids’ file?

Looking forward to your reply.

Thank you very much!

Hi, thanks for this amazing resource! I downloaded the gene count matrix and started exploring the data. Your website says,

Parsing the expression matrix might be long due to its size.
If you are using R, the .tsv files can be parsed using the following instruction:
read.table(path, sep = '\t', stringsAsFactors = F, header = T, row.names = 1)

Just a suggestion: Yes, this fat data frame will take a while to load with base R. But I used vroom, which only took like 3 seconds. I think this suggestion, or using data.table::fread(), would be useful to people who are frustrated by how long it takes to load the data.