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

Hapi_0.0.3.tar.gz
Hapi_0.0.3.zip(r-4.7-any)Hapi_0.0.3.zip(r-4.6-any)Hapi_0.0.3.zip(r-4.5-any)
Hapi_0.0.3.tgz(r-4.6-any)Hapi_0.0.3.tgz(r-4.5-any)
Hapi_0.0.3.tar.gz(r-4.7-any)Hapi_0.0.3.tar.gz(r-4.6-any)
Hapi_0.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Hapi/json (API)

# Install 'Hapi' in R:

install.packages('Hapi', repos = c('https://rli012.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

crossover - Crossover information across all gamete cells
gamete11 - Haplotypes of a single gamete cell for visualization
gmt - Raw genotyping data
hg19 - Chromosome information of hg19

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

snp genomicvariation genetics hiddenmarkovmodel singlecell sequencing microarray

3.89 score 52 scripts 250 downloads 3 mentions 16 exports 18 dependencies

Last updated from:6cd2fcf8cf. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	163
source / vignettes	OK	204
linux-release	OK	184
macos-release	OK	79
macos-oldrel	OK	80
windows-devel	OK	92
windows-release	OK	75
windows-oldrel	OK	75
wasm-release	OK	103

Exports:base2num hapiAssemble hapiAssembleEnd hapiAutoPhase hapiBlockMPR hapiCVCluster hapiCVDistance hapiCVMap hapiCVResolution hapiFilterError hapiFrameSelection hapiGameteView hapiIdentifyCV hapiImupte hapiPhase num2base

Dependencies:cli cpp11 farver ggplot2 glue gtable HMM isoband labeling lifecycle R6 RColorBrewer rlang S7 scales vctrs viridisLite withr

Hapi: an R package for chromosome-length haplotype inference using genotypic data of single gamete cells

Rendered fromHapi.Rmdusingknitr::rmarkdown

Last update: 2018-07-28
Started: 2018-07-28

Help page	Topics
Hapi is a novel easy-to-use package that only requires 3 to 5 gametes to reconstruct accurate and high-resolution haplotypes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and next generation 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 level of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of crossovers in the gametes.	Hapi-package Hapi
Convert genotype coded in A/T/C/G to 0/1	base2num
Crossover information across all gamete cells	crossover
Haplotypes of a single gamete cell for visualization	gamete11
Raw genotyping data	gmt
Consensus haplotype assembly	hapiAssemble
Assembly of haplotypes in regions at the end of a chromosome	hapiAssembleEnd
Automatic inference of haplotypes	hapiAutoPhase
Maximum Parsimony of Recombination (MPR) for proofreading of draft haplotypes	hapiBlockMPR
Filter out hetSNPs in potential complex regions	hapiCVCluster
Histogram of crossover distance	hapiCVDistance
Visualization of crossover map	hapiCVMap
Histogram of crossover resolution	hapiCVResolution
Filter out hetSNPs with potential genotyping errors	hapiFilterError
Selection of hetSNPs to form a framework	hapiFrameSelection
Visualization of haplotypes in a single gamete cell	hapiGameteView
Indentify crossovers in gamete cells	hapiIdentifyCV
Imputation of missing genotypes in the framework	hapiImupte
Phase draft haplotypes by majority voting	hapiPhase
Chromosome information of hg19	hg19
Convert genotype coded in 0/1 to A/T/C/G	num2base

Package: Hapi 0.0.3

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

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)