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bioc
GWASTools:Tools for Genome Wide Association Studies
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
Maintained by Stephanie M. Gogarten. Last updated 15 days ago.
snpgeneticvariabilityqualitycontrolmicroarray
17 stars 10.67 score 396 scripts 5 dependentsbioc
SeqVarTools:Tools for variant data
An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.
Maintained by Stephanie M. Gogarten. Last updated 5 months ago.
snpgeneticvariabilitysequencinggenetics
3 stars 8.76 score 384 scripts 2 dependentsbioc
GBScleanR:Error correction tool for noisy genotyping by sequencing (GBS) data
GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.
Maintained by Tomoyuki Furuta. Last updated 15 days ago.
geneticvariabilitysnpgeneticshiddenmarkovmodelsequencingqualitycontrolcpp
4 stars 5.92 score 6 scripts
svilsen
STRMPS:Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data
Loading, identifying, aggregating, manipulating, and analysing short tandem repeat regions of massively parallel sequencing data in forensic genetics. The analyses and framework implemented in this package relies on the papers of Vilsen et al. (2017) <doi:10.1016/j.fsigen.2017.01.017> and Vilsen et al. (2018) <doi:10.1016/j.fsigen.2018.04.003>. Note: that the parallelisation in the package relies on mclapply() and, thus, speed-ups will only be seen on UNIX based systems.
Maintained by Søren B. Vilsen. Last updated 19 days ago.
biostringspwalignshortreadiranges
4.30 score