myvariant

The IGVF Catalog provides data on the impact of genomic variants on function. The `rigvf` package provides an interface to the IGVF Catalog, allowing easy integration with Bioconductor resources.

The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.

This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.

Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).

svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.