Package: parati 1.0.0

Jinyi Che

parati: Parental Allele Transmission Inference for Trio Genotype Data

Infers maternal and paternal transmitted and non-transmitted alleles from phased trio genotype data. The package supports SNP-level analyses of genetic nurture and transgenerational effects. It interoperates with Bioconductor VCF infrastructure through support for VariantAnnotation::VCF objects and returns R objects for downstream analysis.

Authors:Jinyi Che [aut, cre]

parati_1.0.0.tar.gz
parati_1.0.0.zip(r-4.7)parati_1.0.0.zip(r-4.6)parati_1.0.0.zip(r-4.5)
parati_1.0.0.tgz(r-4.6-any)parati_1.0.0.tgz(r-4.5-any)
parati_1.0.0.tar.gz(r-4.7-any)parati_1.0.0.tar.gz(r-4.6-any)
parati_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
parati/json (API)
NEWS

# Install 'parati' in R:

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

Bug tracker:https://github.com/newche/parati/issues

On BioConductor:parati-1.1.0(bioc 3.24)parati-1.0.0(bioc 3.23)

genetics snp sequencing variantannotation software

4.40 score 232 downloads 6 exports 98 dependencies

Last updated from:4abcfd9e58 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	181
linux-devel-x86_64	OK	294
source / vignettes	OK	298
linux-release-x86_64	OK	325
macos-release-arm64	OK	205
macos-oldrel-arm64	OK	197
windows-devel	OK	274
windows-release	OK	273
windows-oldrel	OK	269
wasm-release	OK	158

Exports:haplotype_infer parati_run read_vcf_by_chr vcf_dt_to_vcfR write_vcf_dt write_vcf_obj

Dependencies:abind AnnotationDbi ape askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli cluster codetools cpp11 crayon curl data.table DBI DelayedArray digest dplyr fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise memuse mgcv mime nlme openssl openxlsx permute pillar pinfsc50 pkgconfig png R.methodsS3 R.oo R.utils R6 Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vcfR vctrs vegan viridisLite withr XML XVector yaml zip

PARATI: Parental Allele Transmission Inference

Jinyi Che

Rendered fromparati-workflow.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-14
Started: 2026-01-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Infer parental transmitted and non-transmitted alleles	haplotype_infer
Run PARATI inference workflow	parati_run
Read VCF by chromosome	read_vcf_by_chr
Convert data.table to vcfR object	vcf_dt_to_vcfR
Write VCF data.table to file	write_vcf_dt
Write vcfR object to file	write_vcf_obj