[Bioc-devel] Submission: PARATI v0.99.0

[Kern, Lori]

You should submit to the formal Bioconductor package review. See https://github.com/Bioconductor/Contributions/


Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Jinyi Che <chejinyi777 using gmail.com>
Sent: Friday, January 16, 2026 9:36 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Submission: PARATI v0.99.0

Dear Bioconductor developers,

I would like to submit my R/Bioconductor package **PARATI** for review.

Package name: PARATI
Version: 0.99.0
GitHub repository: https://secure-web.cisco.com/1ULDHA7tAwm4N5CdbrjBEauLtG650jpYoNKd5f-ctlSWGXwepyjyrTPbI-1X3bq9E0-4cq4_z0H3kyMV2XCOsJtEwO98eq1PevjEKCQzGddl12K-dULKAfNH8nJiRsxCVX2nui4EUZ_Jc6gXecj-Auw3Bg75ATgPSifDlzYmIjoDkVsqvT3iJwnV6wzwYR_F95zr_fwk4rLcQbzM0NRkaIOuqMwwEZYbYzUVOqkznq2HLk60CtFJj8RPK0xPovngwCLKJaEzurnUjxfhuXWJWlexESrKBNxhGbwhpysTJ2khLSt1wIsz1Je40hxsWPcJ0/https%3A%2F%2Fgithub.com%2Fnewche%2FPARATI
R version: � 4.1
Bioconductor compatibility: tested with current release

**Description:**
PARATI infers maternal and paternal transmitted and non-transmitted alleles
from trio genotype data.
It enables SNP-specific analyses of genetic nurture and transgenerational
effects. The package supports homozygous trios, mixed
homozygote/heterozygote, and triple heterozygotes using haplotype
similarity with a user-defined window.

**Dependencies:**
- Imports: data.table, dplyr, stringr, optparse, openxlsx, vcfR, methods
- Suggests: knitr, rmarkdown, BiocStyle, testthat
- Optional: PLINK 1.9 (for exporting PLINK bed/bim/fam files)

**Vignette and Examples:**
- The package contains a vignette `parati-workflow.Rmd` demonstrating a
minimal example using the included testing dataset
(`Toy_TrioGenotype.vcf.gz` and `Toy_FamilyIndexTable.xlsx`).

**Testing:**
- R CMD check completed successfully without errors.
- All example code and vignettes run correctly.
- Testthat unit tests are included and pass.

**Additional notes:**
- This package is intended for analysis of autosomal biallelic SNPs in
trios.
- Sample IDs in the VCF must match the FamilyIndex table.
- Quality control is recommended prior to running PARATI (call rate, MAF,
Mendelian inconsistencies).

Please let me know if you require any additional information.
Thank you for your consideration.

Best regards,
Jinyi Che
Email: chejinyi777 using gmail.com
GitHub: https://secure-web.cisco.com/1ULDHA7tAwm4N5CdbrjBEauLtG650jpYoNKd5f-ctlSWGXwepyjyrTPbI-1X3bq9E0-4cq4_z0H3kyMV2XCOsJtEwO98eq1PevjEKCQzGddl12K-dULKAfNH8nJiRsxCVX2nui4EUZ_Jc6gXecj-Auw3Bg75ATgPSifDlzYmIjoDkVsqvT3iJwnV6wzwYR_F95zr_fwk4rLcQbzM0NRkaIOuqMwwEZYbYzUVOqkznq2HLk60CtFJj8RPK0xPovngwCLKJaEzurnUjxfhuXWJWlexESrKBNxhGbwhpysTJ2khLSt1wIsz1Je40hxsWPcJ0/https%3A%2F%2Fgithub.com%2Fnewche%2FPARATI

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