- Documentation · Repository · DOI
- ⸻ #1
readfcs: Read FCS files#
readfcs is a lightweight open-source Python package that loads data and metadata from Flow Cytometry Standard (FCS) files into
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
readfcs is used by pytometry [Buttner22].
We are grateful to Maren Büttner for valuable discussions.
Cite the software and this report as:
Sun S & Wolf A (2022). readfcs: Read FCS files. Lamin Blog. https://doi.org/10.56528/rfcs
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.
Previous: Hello world! Next: nbproject: Manage Jupyter notebooks