Tool:PIASO, a python toolkit for single-cell data analysis

Question

[Min]

Hi,

We have recently released our PIASO, a python toolkit for single-cell data analysis.

GitHub: https://github.com/genecell/PIASO

API and tutorials: https://genecell.github.io/PIASO

Here is a snapshot of PIASO documentation (Feb 26, 2025):

and here is a snapshot of PIASO GitHub (Feb 26, 2025):

For now, PIASO could be install via pip:

pip install piaso-tools

and the development version could be installed via:

 pip install git+https://github.com/genecell/PIASO.git

Thank you! Looking forward to hearing your feedbacks and suggestions!

Best,

Min

[LChart]

This introduces quite a few (seemingly) new approaches to the processing of single-cell data:

• COSG variable selection

• INFOG normalization

• GDR embedding

which don't appear to have individual references in the documentation, nor are workings of these algorithms are not detailed in the API docs. It would definitely be helpful to have these; and some basic examples in the docstrings themselves. For instance: do I have to run INFOG first before GDR? Will it do so automatically? (etc)

[LChart]

Also I tried runGDR as in the vignette using an environment with pip install piaso-tools and got an error that a csr matrix does not have an attribute .A arising from cosg. In scipy 1.14 the.A attribute was removed from sparse matrices; so there is an undocumented upper version dependency.

Edit: It also fails if the index names are not unique.

[Min]

Thank you so much! We will fix the errors and updated the codes!

[Min]

The issues were now fixed in piaso-tools v1.0.1 in PyPI and cosg v1.0.3 in PyPI. Thank you for your feedback and suggestion!