Package: Hapi 0.0.3

Hapi: Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

Inference of chromosome-length haplotypes using a few haploid gametes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

Authors:Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, Le Zhang, Julong Wei, Sergio Pietro Ferrante, Mikeal L. Roose, Zhenyu Jia

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16 exports 1.00 score 29 dependencies 3 mentions 41 scripts 150 downloads

Last updated 6 years agofrom:6cd2fcf8cf. Checks:OK: 7. Indexed: yes.

Exports:base2numhapiAssemblehapiAssembleEndhapiAutoPhasehapiBlockMPRhapiCVClusterhapiCVDistancehapiCVMaphapiCVResolutionhapiFilterErrorhapiFrameSelectionhapiGameteViewhapiIdentifyCVhapiImuptehapiPhasenum2base

Dependencies:clicolorspacefansifarverggplot2gluegtableHMMisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr