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hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
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How to load 10x data (.tsv files) into scde? #54

Closed rgupta122 closed 5 years ago

rgupta122 commented 6 years ago

Can the output from 10x chromium be loaded into scde as a data frame? The output is 3 files: barcodes.tsv genes.tsv matrix.mtx

pkharchenko commented 6 years ago

We generally recommend using pagoda2 (https://github.com/hms-dbmi/pagoda2 https://github.com/hms-dbmi/pagoda2) for 10x data. In any case, this tutorial shows how to read in a count matrix from such files (see t.load.10x.data() usage): http://pklab.med.harvard.edu/peterk/p2/walkthrough.nb.html http://pklab.med.harvard.edu/peterk/p2/walkthrough.nb.html

Best, -peter.

On Nov 5, 2017, at 10:30 AM, rgupta122 notifications@github.com wrote:

Can the output from 10x chromium be loaded into scde as a data frame? The output is 3 files: barcodes.tsv genes.tsv matrix.mtx

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