flowAI Flow Cytometry Data Cleaning using R: A Step-by-step Tutorial
Welcome to this comprehensive tutorial on cleaning Flow Cytometry Standard (FCS) files using R packages, flowCore, and flowAI. We explore automating the cleaning process for FCS files in a specified directory and how to save the cleaned files automatically. This video is perfect for researchers and anyone interested in automating flow cytometry data cleaning!
*🔑 What you'll learn:*
Installing required packages.
Automating the reading of FCS files.
Applying flowAI quality control.
Writing cleaned FCS files back.
*⚙️ Installation & Resources:*
1. *R:*
[Download & Install](https://cran.r-project.org/)
R is a language and environment for statistical computing and graphics.
2. *R Studio:*
[Download & Install](https://www.rstudio.com/products/rstu...)
R Studio is an integrated development environment (IDE) for R.
3. *BiocManager:*
[Installation Guide](https://www.bioconductor.org/install/...)
BiocManager provides access to Bioconductor packages.
4. *flowCore:*
[Installation Guide & Documentation](https://bioconductor.org/packages/rel...)
flowCore is a Bioconductor package for basic flow cytometry data processing.
5. *flowAI:*
[Installation Guide & Documentation](https://bioconductor.org/packages/rel...)
flowAI is used for automatic and interactive quality control of flow cytometry data.
6. *Script Used in this Tutorial:*
[Download the R Script](https://drive.google.com/file/d/1YTsg...)
*🔬 Flow Data Analysis Software:*
Refer to the links in the list for various flow data analysis software options available. Some offer free versions and are user-friendly, catering to different needs in flow cytometry data analysis.
*📈 Automation of the Script:*
This script is automated to read all FCS files in a directory, apply quality control, and write back the cleaned files to a new directory. It makes handling multiple FCS files efficient and error-free, ensuring high-quality data for subsequent analysis.
*💬 Comments:*
If you have any questions, suggestions, or comments, please feel free to leave them below. We value your feedback to deliver content that caters to your needs!
*Flow Data Analysis Software:*
1. [FlowJo](https://www.flowjo.com/)
2. [FCSExpress7](https://denovosoftware.com/)
3. [CellEngine](https://cellengine.com/?utm_source=Fl...)
4. [NovoExpress](https://www.agilent.com/en/product/re...)
5. [WinList](https://www.vsh.com/products/winlist/)
6. [iQue Forecyt](https://www.sartorius.com/en/products...)
7. [BD FACSDiva](https://www.bdbiosciences.com/en-us/p...)
8. [CytoBank](https://www.beckman.com/flow-cytometr...)
9. [Flowlogic](https://flowlogic.software/)
10. [Kaluza](https://www.beckman.com/flow-cytometr...)
11. [CellCapture](https://stratedigm.com/cellcapture/)
12. [OMIQ](https://www.omiq.ai/)
13. [Floreada.io (Free Version)](https://floreada.io/)
14. [Red Matter App](https://www.redmatterapp.com/)
15. [PUCL](http://www.cyto.purdue.edu/Purdue_sof...)
16. [CyFlogic](https://www.cyflogic.com/)
17. [Flowing Software](https://bioscience.fi/services/cell-i...)
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