svaNUMT

svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.

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.

StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Annotate variants, compute amino acid coding changes, predict coding outcomes.

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).