flowio

Parse FCS files into NumPy arrays and extract channel metadata.

Updated Mar 10, 2026

Search Tags:#bioinformatics #data parsing #numpy #data preprocessing #flow cytometry #fcs files

Ready to run

npx skills add https://github.com/felixboehm/biochem-allergy --skill flowio-felixboehm

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: flowio
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/flowio
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill flowio-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill simplifies the complex task of reading and processing Flow Cytometry Standard (FCS) files, enabling quick access to critical experimental data.

Core Features & Use Cases

FCS File Parsing: Reads FCS files (versions 2.0-3.1) to extract metadata and event data.
Data Conversion: Converts event data into NumPy arrays for further analysis.
Metadata Extraction: Retrieves channel information, acquisition dates, and instrument details.
Use Case: You have a directory full of FCS files from a recent experiment. Use this Skill to extract the event data from each file and combine it into a single dataset for downstream analysis in Python.

Quick Start

Use the flowio skill to read the file 'experiment.fcs' and print the number of events and channels.

Frequently Asked Questions about flowio

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I parse flow cytometry FCS files into NumPy arrays in Python?▼

To parse flow cytometry FCS files into NumPy arrays, use this Skill to read event data and extract experimental metadata. It handles FCS versions 2.0-3.1 and outputs structured NumPy arrays for downstream analysis.

What metadata can I extract from FCS files during data preprocessing?▼

When parsing FCS files, you can extract metadata including channel information, acquisition dates, and instrument details. This metadata is retrieved alongside event data to facilitate cytometry analysis.

Does this FCS file parser support older flow cytometry data formats?▼

Yes, this FCS file parser supports older flow cytometry data formats, specifically reading FCS versions 2.0 through 3.1. It handles common file parsing issues across these versions to extract event data.

Can I batch process a directory of FCS files and combine the event data?▼

You can batch process a directory of FCS files by using the Skill to extract event data from each file. It converts events into NumPy arrays, which can then be combined into a single dataset for analysis.

What are common limitations when parsing FCS files for bioinformatics analysis?▼

Common limitations when parsing FCS files involve handling version-specific parsing issues across different cytometry standards. This Skill addresses common file parsing errors for FCS versions 2.0-3.1 to ensure event data extraction.