HumanBase Review Raper updates #9
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Add link to SEI paper (2022) at the end of the first paragraph in the Output section to provide users with detailed information about how SEI sequence scores are computed.
Add description of regulatory feature scores and ExPecto expression effect with references to DeepSEA (Beluga) model and ExPecto paper (2018).
Make 'Regulatory feature scores:' and 'ExPecto expression effect:' bold for better readability and consistency.
- Remove 'usage' page from table of contents - Add 'clever' (ExPectoSC) page to table of contents - Fix ExPectoSC title formatting and website overview underline - Add html_context configuration for ReadTheDocs - Remove deprecated html_theme_path configuration
Move variant analysis description from Method Details to new Output section. Add explanation of z-score normalization and reliability guidelines with reference to ExPectoSC paper (2023).
- Extract In Silico Mutagenesis section from beluga.rst to its own file - Add output section with log2 fold change equation and DeepSEA paper reference - Add new page to table of contents - Improve sentence flow by placing equation after variable definitions
- Add .readthedocs.yaml with Python 3.10 and Ubuntu 22.04 build settings - Add docs/requirements.txt with Sphinx dependencies - Fixes Read the Docs build error about missing configuration file
- Create parameterized common include files for input format documentation - Add new Seqweaver documentation page for 1000bp sequence model - Extract common file format descriptions to _includes/common-input-formats.rst - Extract genome coordinates and submission info to _includes/common-submission-info.rst - Update format names to capitals (VCF, FASTA, BED) - Add FASTA format explanation with example structure - Add general recommendation: FASTA input smaller than required length not recommended unless very close - Include padding behavior warnings and note about N's rarity in training data
Edits to seqweaver.
Documentation edits
- always show year last updated - remove RTD mention and Sphinx mention - remove Related tools section from use cases
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