cyto

README

cyto

Cyto is a Go library for cytometry data analysis.

• It provides tools to parse, process, and analyze Flow Cytometry Standard (FCS) files (FCS 3.1 standard).

📦 Features

• Read and parse .fcs files
• Access FCS metadata and event data
• Command-line interface for basic operations

🛠️ Installation

Prerequisites

• Go

Using Go Get

go get github.com/immunoconductor/cyto@latest

The binary will be placed in $GOBIN (default: $HOME/go/bin). Make sure that directory is in your PATH:

export PATH="$PATH:$(go env GOPATH)/bin"

Clone Repository

git clone https://github.com/immunoconductor/cyto.git
cd cyto
go build

Import as Module

Add it to your module by importing:

import "github.com/immunoconductor/cyto/fcs"

Then run:

go mod tidy

📋 Usage

Command Line Interface

Convert FCS files to CSV format:

cyto fcs -i example.fcs -o example.csv

Convert FCS files to CSV format with transformation and shortnames for headings:

cyto fcs -i example.fcs -o example.csv --transform --shortnames

Output names:

cyto fcs -i example.fcs --names

Options:

• -i: Input FCS file path
• -o: Output CSV file path
• --transform: Apply arcsinh transformation to the data
• --shortnames: Use short names (concise identifiers)
• --names: Output names (channel identifiers)

Go Library Example

import "github.com/immunoconductor/cyto/fcs"

func main() {
    fcs, err := fcs.Read("fcs3.1.fcs", false)
    if err != nil {
        t.Errorf(err.Error())
    }

    fmt.Println(fcs.Names())
}

📊 Documentation

Documentation is currently under development. For now, please refer to the code comments and examples in this README.

🔄 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add some amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

📄 License

This project is licensed under the GPL-3 License - see the LICENSE file for details.

🙏 Acknowledgments

• Contributors to the project
• The Flow Cytometry community