Genome Structure Rearrangement Calling in Genomes with High Synteny

Pipeline to read and analyze raw SNP array data. The data is preprocessed and normalized. Genotypes and CNVs are called. Synteny blocks are calculated and translocations detected. The results can be plotted with special functions.


Updated version which will be released to CRAN

added technical descriptions to vignettes

plot_cnv parameters added moved some packages from Suggests to Depends

filter_cnv function added plot_cnv function added

Bead and SD information from raw data are now supported in the normalized data

Unit testing with testthat Code reformated Semantic versioning NEWS file included

First release

Reference manual

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1.1 by Fabian Grandke, 2 years ago

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Browse source code at

Authors: Fabian Grandke [cre, aut], Birgit Samans [aut]

Documentation:   PDF Manual  

GPL-3 license

Imports illuminaio, limma, preprocessCore, R6, utils, grDevices, graphics, dbscan, Ckmeans.1d.dp, DNAcopy, openxlsx

Suggests testthat, knitr, rmarkdown, brassicaData, mixtools, devtools, KernSmooth

See at CRAN