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bioc
Pedixplorer:Pedigree Functions
Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.
Maintained by Louis Le Nezet. Last updated 18 days ago.
softwaredatarepresentationgeneticsgraphandnetworkvisualizationkinshippedigree
2 stars 6.08 score 10 scriptsbioc
TVTB:TVTB: The VCF Tool Box
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).
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwaregeneticsgeneticvariabilitygenomicvariationdatarepresentationguidnaseqwholegenomevisualizationmultiplecomparisondataimportvariantannotationsequencingcoveragealignmentsequencematching
2 stars 5.76 score 16 scripts
warnes
genetics:Population Genetics
Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...
Maintained by Gregory Warnes. Last updated 4 years ago.
2 stars 5.55 score 374 scripts 5 dependents