How to transform my expression matrix

[QiangShiPKU]

Hello,
I noticed the expression matrix in example_inputs is .npy and .p format. However, my expression matrix is matrix.mtx, barcodes.tsv, and genes.tsv from 10X genomics or matrix.txt with row names (genes) and column names (cells). How could I tranform these format to .npy and .p?

[calebweinreb]

Hi, It is best to use the new version of SPRING which is available at https://github.com/AllonKleinLab/SPRING_dev. We have an ipython notebook for beginning with 10X data files. Sam do you mind sending this?

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On Sat, Aug 11, 2018 at 10:44 PM, Qiang ***@***.***> wrote: Hello, I noticed the expression matrix in example_inputs is .npy and .p format. However, my expression matrix is matrix.mtx, barcodes.tsv, and genes.tsv from 10X genomics or matrix.txt with row names (genes) and column names (cells). How could I tranform these format to .npy and .p? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF3OsgwY_pliLc9ajUae8i8BpydqxGf0ks5uP5Z1gaJpZM4V5Yew> .

[swolock]

You should be able follow this example jupyter notebook to build a (new version) SPRING plot from your 10X data. Let us know if you run into any issues.

[QiangShiPKU]

Thanks，I will try