Updating Sage Binaries

[JohannesvKL]

User description

Updates Sage binaries for Mac, Windows and Linux to v0.14.7, the latest release. Allows for annotation of Spectra.

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PR Type

documentation

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Description

• Added a new "Interoperability" section to the Sage README file, detailing how Sage integrates with various open-source proteomics tools and projects.
• Listed several projects that support analyzing results from Sage or redistribute Sage binaries, enhancing the documentation for users.
• Encouraged users to contribute by adding their projects if they support Sage, fostering community engagement.

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Changes walkthrough 📝

	Relevant files
Documentation	README.md Add interoperability section and related project links      Windows/64bit/Sage/README.md Added a new section on interoperability. Listed projects that support or integrate with Sage. Updated links to related projects and tools. Encouraged contributions for additional project support. +13/-1

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PR Code Suggestions ✨

Category	Suggestion	Score
Enhancement	Add brief descriptions of how Sage integrates with or supports each listed project to provide more context for users Consider adding a brief description of how Sage integrates with or supports each listed project to provide more context for users. Windows/64bit/Sage/README.md [57-64] -- [SearchGUI](http://compomics.github.io/projects/searchgui): a graphical user interface for running searches -- [PeptideShaker](http://compomics.github.io/projects/peptide-shaker): visualize peptide-spectrum matches -- [MS2Rescore](http://compomics.github.io/projects/ms2rescore): AI-assisted rescoring of results -- [Picked group FDR](https://github.com/kusterlab/picked_group_fdr): scalable protein group FDR for large-scale experiments -- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library -- [quantms](https://github.com/bigbio/quantms): nextflow pipeline for running searches with Sage -- [OpenMS](https://github.com/OpenMS/OpenMS): Sage is included as a "TOPP" tool in OpenMS -- [sager](https://github.com/UCLouvain-CBIO/sager): R package for analyzing results from Sage searches +- [SearchGUI](http://compomics.github.io/projects/searchgui): a graphical user interface for running searches, including Sage as a search engine option +- [PeptideShaker](http://compomics.github.io/projects/peptide-shaker): visualize peptide-spectrum matches, compatible with Sage search results +- [MS2Rescore](http://compomics.github.io/projects/ms2rescore): AI-assisted rescoring of results, can process Sage output for improved scoring +- [Picked group FDR](https://github.com/kusterlab/picked_group_fdr): scalable protein group FDR for large-scale experiments, supports Sage result files +- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library, enabling direct integration of Sage functionality in Python scripts +- [quantms](https://github.com/bigbio/quantms): nextflow pipeline for running searches with Sage, streamlining the analysis workflow +- [OpenMS](https://github.com/OpenMS/OpenMS): Sage is included as a "TOPP" tool in OpenMS, allowing seamless integration with other OpenMS tools +- [sager](https://github.com/UCLouvain-CBIO/sager): R package for analyzing results from Sage searches, facilitating post-processing and visualization in R Apply this suggestion Suggestion importance[1-10]: 8 Why: Providing context on how Sage integrates with each project significantly enhances user understanding and the practical application of the information, making it a valuable enhancement.	8
	Add version numbers or release dates to the listed projects for better clarity on compatibility and recency Consider adding version numbers or release dates for the listed projects to provide users with information about compatibility and recency. Windows/64bit/Sage/README.md [57-64] -- [SearchGUI](http://compomics.github.io/projects/searchgui): a graphical user interface for running searches -- [PeptideShaker](http://compomics.github.io/projects/peptide-shaker): visualize peptide-spectrum matches -- [MS2Rescore](http://compomics.github.io/projects/ms2rescore): AI-assisted rescoring of results -- [Picked group FDR](https://github.com/kusterlab/picked_group_fdr): scalable protein group FDR for large-scale experiments -- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library -- [quantms](https://github.com/bigbio/quantms): nextflow pipeline for running searches with Sage -- [OpenMS](https://github.com/OpenMS/OpenMS): Sage is included as a "TOPP" tool in OpenMS -- [sager](https://github.com/UCLouvain-CBIO/sager): R package for analyzing results from Sage searches +- [SearchGUI](http://compomics.github.io/projects/searchgui) (v2.9.0): a graphical user interface for running searches +- [PeptideShaker](http://compomics.github.io/projects/peptide-shaker) (v2.0.0): visualize peptide-spectrum matches +- [MS2Rescore](http://compomics.github.io/projects/ms2rescore) (v0.2.1): AI-assisted rescoring of results +- [Picked group FDR](https://github.com/kusterlab/picked_group_fdr) (v1.0.2): scalable protein group FDR for large-scale experiments +- [sagepy](https://github.com/theGreatHerrLebert/sagepy) (v0.1.0): Python bindings to the sage-core library +- [quantms](https://github.com/bigbio/quantms) (v1.1.0): nextflow pipeline for running searches with Sage +- [OpenMS](https://github.com/OpenMS/OpenMS) (v2.8.0): Sage is included as a "TOPP" tool in OpenMS +- [sager](https://github.com/UCLouvain-CBIO/sager) (v0.2.0): R package for analyzing results from Sage searches Apply this suggestion Suggestion importance[1-10]: 5 Why: Adding version numbers can help users understand the compatibility and recency of the projects, but it is not crucial for the functionality or understanding of the document.	5
Maintainability	Group the listed projects by their primary function or type to improve organization and readability Consider grouping the listed projects by their primary function or type (e.g., GUI tools, analysis tools, language bindings) to improve readability and organization. Windows/64bit/Sage/README.md [57-64] +GUI Tools: - [SearchGUI](http://compomics.github.io/projects/searchgui): a graphical user interface for running searches - [PeptideShaker](http://compomics.github.io/projects/peptide-shaker): visualize peptide-spectrum matches + +Analysis Tools: - [MS2Rescore](http://compomics.github.io/projects/ms2rescore): AI-assisted rescoring of results - [Picked group FDR](https://github.com/kusterlab/picked_group_fdr): scalable protein group FDR for large-scale experiments -- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library - [quantms](https://github.com/bigbio/quantms): nextflow pipeline for running searches with Sage - [OpenMS](https://github.com/OpenMS/OpenMS): Sage is included as a "TOPP" tool in OpenMS + +Language Bindings: +- [sagepy](https://github.com/theGreatHerrLebert/sagepy): Python bindings to the sage-core library - [sager](https://github.com/UCLouvain-CBIO/sager): R package for analyzing results from Sage searches Apply this suggestion Suggestion importance[1-10]: 7 Why: Grouping projects by function or type enhances readability and organization, making it easier for users to find relevant tools, which is a valuable improvement for maintainability.	7