Improve the clarity of documentation

[stemangiola]

Documentation was improved by:

• Creating CONTRIBUTING.md to provide comprehensive guidelines for community contributions, including bug reporting, enhancement suggestions, development setup, coding style, and commit conventions.
• Creating FAQ.md to address common questions, installation, usage, troubleshooting, and integration with other Bioconductor packages.
• Updating README.Rmd to enhance its structure and content:
  • Added a logo and restructured the introduction with key features and resources.
  • Expanded the function reference with detailed tables for dplyr, tidyr, and visualization functions, including examples.
  • Included new sections for advanced analysis, use cases, and performance tips.
• Significantly enhancing vignettes/introduction.Rmd to serve as a more comprehensive tutorial:
  • Expanded sections on the package's purpose, data structure, and basic operations (filtering, transformation, summarization).
  • Added detailed explanations and examples for advanced analysis, Bioconductor tool integration, complex reshaping, and various visualizations.
  • Included best practices and performance considerations.

These changes aim to make the package documentation more organized, comprehensive, and user-friendly for both new users and potential contributors.