Another requirement

[scriscio]

It looks like the module fcsparser is another requirement to this program. Possibly add to the readme.
https://github.com/eyurtsev/fcsparser

Also fcswrite:
https://pypi.org/project/fcswrite/

pip install fcswrite

[Winnie09]

Dear author,

Thanks for developing the software! I have a few questions but did not find clear answer from your paper:

1. is the input a count matrix?
2. is the output a count matix? Has it been normalzed by library size, or log2-transformed?

Thanks!

[sameetmehta]

Hi,
To the best of my understanding the input matrix is generally "count" matrix is obtained from the CyToF instrument. The output file is also a count matrix but it is normalized using the asinh normalization. You can check this by looking at the range of values from each column. For the raw data the range will be very high. For normalized data the range is usually between 0 - 10, and very rarely a bit higher, but never in 0 - 100+.