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Lori Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <[email protected]> on behalf of Jinyi Che <[email protected]> Sent: Friday, January 16, 2026 9:36 AM To: [email protected] <[email protected]> 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: [email protected] GitHub: https://secure-web.cisco.com/1ULDHA7tAwm4N5CdbrjBEauLtG650jpYoNKd5f-ctlSWGXwepyjyrTPbI-1X3bq9E0-4cq4_z0H3kyMV2XCOsJtEwO98eq1PevjEKCQzGddl12K-dULKAfNH8nJiRsxCVX2nui4EUZ_Jc6gXecj-Auw3Bg75ATgPSifDlzYmIjoDkVsqvT3iJwnV6wzwYR_F95zr_fwk4rLcQbzM0NRkaIOuqMwwEZYbYzUVOqkznq2HLk60CtFJj8RPK0xPovngwCLKJaEzurnUjxfhuXWJWlexESrKBNxhGbwhpysTJ2khLSt1wIsz1Je40hxsWPcJ0/https%3A%2F%2Fgithub.com%2Fnewche%2FPARATI [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://secure-web.cisco.com/1wAgPNfgoBi7_KkcC8sNKrM4CGl4g30pql1BRjsIoMYDS96LtowcwwX4hoi3SIPnW_120--W1XEn7guNmK0NRpADJqi_HtOAVpSWdi-Tk4W0Ht7jh4RE2_8sQFgiwbg-6u8l4a4HlEeizltQLempUpJl5p-PcARsDn-E5d5cuNKK9m8TNzjpGLzNIg3PZQ9IvDXs3oOFBErCsU4Oyo6g2YqmeZ98i2XGmMDvgjg-xGlwxHoF5BlyFC3lIw6axsyXNLdAwdiRNz2a0IkMSDJlKcZjJLdRfYWJ8jgYLFDl8FsWjbC8DZemNLibo-rGcsXsx/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]]
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