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changwn / scFEA

single cell Flux Estimation Analysis (scFEA) Try the below web server!
http://scflux.org/
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Input types #3

Open Hrovatin opened 3 years ago

Hrovatin commented 3 years ago

Could you add some documentation on what kind of inputs/file formats the tool accepts, e.g. expanding descriptions in


python src/scFEA.py --help
changwn commented 3 years ago

More explanations are provided in the help option. Please check and run example data. You just need an SC gene expression matrix for input and do not need to change moduleGene and stoichiometry matrix parameters.

Hrovatin commented 3 years ago

I think that --test_file should be extended - e.g. noting that input for expression is CSV.

changwn commented 3 years ago

Thank you for the suggestion @Hrovatin . For Smart-seq, some data provided on Gene Expression Omnibus (GEO) are txt format (example) thus I suggest the user transform data by themself. Since the computational tool are supposed to be run by a technician, we will not provide an interface for the smart-seq dataset. But we are planning a user-friendly web server in the future for biologists and doctors. For 10x chromium, I will extend the input interface to match the standard pipeline output. If you wish to contribute to this part, I can review it and merge into the master branch after accepted.

Hrovatin commented 3 years ago

I think you can add 10x reading function from Compass, they seem to have similar inputs https://github.com/YosefLab/Compass/blob/abc4456e0b4752b581b3fdfa68882d72e60ab307/compass/utils.py#L56

Hrovatin commented 3 years ago

Also, can you note whether the input should be raw counts, normalised counts, or normalised+log transformed counts.

changwn commented 3 years ago

Also, can you note whether the input should be raw counts, normalised counts, or normalised+log transformed counts.

Thanks. The input can be raw counts or normalized counts. If the value greater than 30, we take log(value + 1 ) for raw counts. The instruction also added in --help function.

Hrovatin commented 3 years ago

Does this mean I can also input log-transformed normalised raw counts?

changwn commented 3 years ago

Does this mean I can also input log-transformed normalised raw counts?

Yes, you can input log-transformed normalized counts.

yanwu2014 commented 2 years ago

Just wanted to echo that it'd be great if the input format was specified a bit more in the docs. Also csvs become pretty unwieldy with large datasets so reading in 10X mtx format would also be helpful