## readfcs: Read FCS files

readfcs is a lightweight open-source Python package that loads data
and metadata from Flow Cytometry Standard (FCS) files into "DataFrame"
and "AnnData" objects, allowing users to flexibly use downstream
analytical tools.

With this, it fills a gap among existing FCS readers in the Python
ecosystem: These are either part of comprehensive analytical packages
(e.g., FlowIO by White21, cytopy by Burton21) that operate on data
structures tailored to specific downstream analyses or they do not
offer support for "AnnData" objects [Yurtsev22].

For the main data and metadata functionality, readfcs builds on
fcsparser [Yurtsev22]. In addition to "FCSParser", readfcs offers
compensation, indexing channels by markers, and structuring metadata
in "AnnData".

readfcs is used by pytometry [Buttner22].

# Acknowledgments

We are grateful to Maren Büttner for valuable discussions.

# Author contributions

Sunny & Alex conceived the project. Sunny developed the software.

# Citation

If you use the results of this work in an academic context, we'd be
happy if you cite "readfcs" and this report as:

 Sun S & Wolf A (2022). readfcs: Read FCS files. Lamin Blog. https://doi.org/10.56528/rfcs

# References

Yurtsev E (2022). FCSParser - a python package for reading fcs files.
GitHub.

White S, Quinn J, Enzor J, Staats J, Mosier S M, Almarode J, Denny T
N, Weinhold K J, Ferrari G & Chan C (2021). FlowKit: A Python toolkit
for integrated manual and automated cytometry analysis workflows.
Frontiers in Immunology, 12. GitHub.

Burton R (2021). CytoPy - a cytometry analysis framework for Python.
GitHub.

Büttner M, Hempel F, Ryborz T, Theis FJ & Schultze JL (2022).
Pytometry: Flow & mass cytometry analytics. bioRxiv. GitHub.