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songlab-cal / rna-sieve

A library for the deconvolution of bulk cell samples using single-cell RNA expression data.

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installation errors

mooreann opened this issue · comments

commented

Is there an alternate way to install or certain dependency packages it relies on that I may not have? Heres the installation error I'm getting:

(base) [mooreank@lngnode2 ~]$ pip3 install rna-sieve
ERROR: Could not find a version that satisfies the requirement rna-sieve (from versions: none)
ERROR: No matching distribution found for rna-sieve
(base) [mooreank@lngnode2 ~]$ pip install rna-sieve
ERROR: Could not find a version that satisfies the requirement rna-sieve (from versions: none)
ERROR: No matching distribution found for rna-sieve

commented

Also how should data be formatted? Genes x samples? Are you going to put your example data up soon?

commented

Apologies, that was a typo, you can install the package at rnasieve not rna-sieve. The example data will not be uploaded to this repository, but the .h5ad can be found freely from the Tabula Muris Senis AWS bucket here: https://s3.console.aws.amazon.com/s3/buckets/czb-tabula-muris-senis/. The example notebook uses files from there without modification.

commented

Also how should data be formatted? Genes x samples? Are you going to put your example data up soon?

From cell [5] in the notebook it appear that it is "genes x samples".