scRNA seq analysis

Hi,

I’m trying to perform scRNA seq analysis using data downloaded from this link.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4952363

There are 3 filtered data files: matrix, barcodes and features.

The first step in the workflow I’m following is data loading which I have attached and the code is below.

library(TENxPBMCData)
all.sce <- list(
    pbmc3k=TENxPBMCData('pbmc3k'),
    pbmc4k=TENxPBMCData('pbmc4k'),
    pbmc8k=TENxPBMCData('pbmc8k')
)

However, I don’t understand the first package they have loaded. Since my data does not contain counts from PBMC cells.

Does anyone know how I might read in the data while still following this pipeline?

http://bioconductor.org/books/3.14/OSCA.multisample/human-pbmcs-10x-genomics.html#ref-zheng2017massively

scrnaseq

• 1,236 views • link

updated 3.7 years ago by Ram

• written 3.7 years ago by bioinformatics •

Start the OSCA tutorials from the beginning, learn to read data and do the basic processing. It's all in there. Don't start with the multi-sample advanced section.

• 0 views • link

written 3.7 years ago by ATpoint

Ok thankyou for this information. Do you know what the lines in this code below mean:

library(DropletTestFiles)
raw.path <- getTestFile("tenx-2.1.0-pbmc4k/1.0.0/raw.tar.gz")
out.path <- file.path(tempdir(), "pbmc4k")
untar(raw.path, exdir=out.path)

library(DropletUtils)
fname <- file.path(out.path, "raw_gene_bc_matrices/GRCh38")
sce.pbmc <- read10xCounts(fname, col.names=TRUE)

• 0 views • link

written 3.7 years ago by bioinformatics •

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