## 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.

# Filling a gap

"readfcs" fills a gap among existing FCS readers in the Python
ecosystem: These are either part of comprehensive analytical packages
(e.g., FlowIO,[1] Cytopy[2]) that operate on data structures tailored
to specific downstream analyses or they do not offer support for
"AnnData" objects.[3]

For the main data and metadata functionality, readfcs builds on
"fcsparser".[3] In addition to "FCSParser", readfcs offers
compensation, indexing channels by markers, and structuring metadata
in "AnnData".

"readfcs" is used by "pytometry".[4]

# 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

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[1] White S, Quinn J, Enzor J, Staats J, Mosier SM, Almarode J, Denny
 TN, Weinhold KJ, Ferrari G & Chan C (2021). FlowKit: A Python
 toolkit for integrated manual and automated cytometry analysis
 workflows. Frontiers in Immunology, 12. GitHub.

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

[3] Yurtsev E (2022). FCSParser - a Python package for reading FCS
 files. GitHub.

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