Changelog • AlphaMissenseR

AlphaMissenseR 1.2.0

(v. 1.1.9) Manage duckdb connections more completely; all registered connections are disconnected (invalidated) whenever a new table is created.
(v. 1.1.7) Add ‘Benchmarking with ProteinGym’ vignette to benchmark AlphaMissense predictions. https://github.com/mtmorgan/AlphaMissenseR/pull/8. Thank you @tram-nguyen-n
(v. 1.1.6) Add gosling_plot() for visualizing variants as bar or lollipop plots. Merges https://github.com/mtmorgan/AlphaMissenseR/pull/6 Thanks @lee-t.
(v. 1.1.4) Add clinvar_data() and clinvar_plot() for visualizing ClinVar data. Merges https://github.com/mtmorgan/AlphaMissenseR/pull/4 Thanks @tram-nguyen-n
(v. 1.1.2) af_predictions() returns a tibble with 21 columns, instead of 20. Merges https://github.com/mtmorgan/AlphaMissenseR/pull/3.

(v. 0.99.21) Update Zenodo data source to record 10813168, with more accessible ‘CC-BY-4.0’ license.
(v. 0.99.16) Housekeeping
- Order vignettes introduction, visualization, issues.
- Use rjsoncons (>= 1.0.1), so that jsonlite is not a hard dependency.
- Acknowledge additional funding sources; add ImmunoOncology biocViews term.
(v. 0.99.15) Respond to Bioconductor reviewer comments
- Use BiocBaseUtils for input assertions.
- Include range join SQL directly rather than via a non-exported function.
- Report file size when downloading.
- Improve test coverage.
- See GitHub issue comment; thanks @LiNk-NY
(v. 0.99.11) Use an S4 class for alphamissense_connection, extending duckdb_connection.
(v. 0.99.10) Introduce visualization on AlphaFold predictions.
(v. 0.99.9) Update maintainer email address, add ‘Resource unavailable’ section to ‘Issues & Solutions’ vignette.
(v. 0.99.7) Update to revised Zenodo API.
(v. 0.99.5) BREAKING change. Requires duckdb >= 0.9.1, which cannot read DuckDB databases created with earlier versions. Also introduces changes to local cache naming. See the ‘Issues & Solutions’ vignette.
(v. 0.99.4) Change back to Bioconductor ‘Software’ package, to allow for regular testing of data access code.
(v. 0.99.1) Change to Bioconductor ‘Annotation’ package.
(v. 0.99.1) Update to change in Zenodo API.

(v. 0.0.18) Rename (including updating existing tables) ‘#CHROM’ to ‘CHROM’ in hg19 / hg38 tables
(v. 0.0.17) Initial Bioconductor submission.