{ "_id": "6adb1b1b55731c523ae76244", "Package": "geneNR", "Title": "Automated Gene Identification for Post-GWAS and QTL Analysis", "Version": "3.0.0", "Authors@R": "c(person(\"Rajamani\", \"Nirmalaruban\", role = c(\"aut\", \"cre\", \"cph\"), email = \"nirmalaruban97@gmail.com\"),\nperson(\"R.\", \"Suvitha\", role = \"aut\", email = \"suvitha59528@gmail.com\"),\nperson(\"Rajbir\", \"Yadav\", role = \"aut\", email = \"rajbiryadav@yahoo.com\"),\nperson(\"Meda\", \"Alekya\", role = \"aut\", email = \"alekyameda210pink@gmail.com\"),\nperson(\"Amit Kumar\", \"Mazumder\", role = \"aut\", email = \"amitkumarmazumder434@gmail.com\"),\nperson(\"Thirumurugan\", \"Sathya\", role = \"aut\", email = \"sathyasuba96@gmail.com\"),\nperson(\"Subramani\", \"Sugumar\", role = \"aut\", email = \"sugustays@gmail.com\"),\nperson(\"Prashanth\", \"babu\", role = \"aut\", email = \"prashanthbabuh@gmail.com\"),\nperson(\"Manjeet\", \"Kumar\", role = \"aut\", email = \"manjeetbhu615@gmail.com\"),\nperson(\"Kiran B\", \"Gaikwad\", role = \"aut\", email = \"gaikwadkb@gmail.com\"),\nperson(\"Naresh Kumar\", \"Bainsla\", role = \"aut\", email = \"Bainsla.breeder.icar@gmail.com\"),\nperson(\"S.\", \"Bhaskar Reddy\", role = \"aut\", email = \"bhaskarreddy1996@gmail.com\"))", "Description": "Facilitates the post-Genome Wide Association Studies\n(GWAS) and Quantitative Trait Loci (QTL) analysis of\nidentifying candidate genes within user-defined search window,\nbased on the identified Single Nucleotide Polymorphisms (SNPs)\nas given by Mazumder AK (2024)\n. It supports candidate gene\nanalysis for wheat and rice. Just import your GWAS result as\nexplained in the sample_data file and the function does all the\nmanual search and retrieve candidate genes for you, while\nexporting the results into ready-to-use output.", "License": "CC BY 4.0", "Copyright": "(C) 2026 Nirmalaruban", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "LazyData": "TRUE", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-23 08:25:56 UTC", "User": "root" }, "Author": "Rajamani Nirmalaruban [aut, cre, cph], R. Suvitha [aut], Rajbir\nYadav [aut], Meda Alekya [aut], Amit Kumar Mazumder [aut],\nThirumurugan Sathya [aut], Subramani Sugumar [aut], Prashanth\nbabu [aut], Manjeet Kumar [aut], Kiran B Gaikwad [aut], Naresh\nKumar Bainsla [aut], S. Bhaskar Reddy [aut]", "Maintainer": "Rajamani Nirmalaruban ", "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev libx11-dev\nzlib1g-dev", "Repository": "https://nirmalaruban.r-universe.dev", "Date/Publication": "2026-07-05 15:10:02 UTC", "RemoteUrl": "https://github.com/cran/geneNR", "RemoteRef": "HEAD", "RemoteSha": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "_user": "nirmalaruban", "_type": "src", "_file": "geneNR_3.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/56202f4d347110a0fc9b6abd08305aef432a4ad22091672e29916399a6a12df0", "_filesize": 258491, "_sha256": "56202f4d347110a0fc9b6abd08305aef432a4ad22091672e29916399a6a12df0", "_expires": "2027-01-31T08:30:17.000Z", "_created": "2026-10-23T08:25:56.000Z", "_published": "2026-10-23T08:30:19.171Z", "_upstream": "https://github.com/cran/geneNR", "_status": "success", "_maintainer": { "name": "Rajamani Nirmalaruban", "email": "nirmalaruban97@gmail.com", "login": "nirmalaruban", "description": "", "uuid": 199979695 }, "_jobs": [ { "job": 120317845430, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12489445361" }, { "job": 120317845406, "time": 125, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12487654523" }, { "job": 120317845490, "time": 215, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12489475076" }, { "job": 120317845292, "time": 212, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12488866820" }, { "job": 120315427333, "time": 374, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12487639307" }, { "job": 120317845486, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12488462807" }, { "job": 120317845397, "time": 76, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12489290452" }, { "job": 120317845466, "time": 84, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12488418772" }, { "job": 120317845384, "time": 87, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12489300158" } ], "_buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486", "_commit": { "id": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "author": "Rajamani Nirmalaruban ", "committer": "cran-robot ", "message": "version 3.0.0\n", "time": 1783264202 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "readr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "rvest", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "writexl", "role": "Imports" }, { "package": "vcfR", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-27", "n": 1 } ], "_tags": [ { "name": "3.0.0", "date": "2026-07-05" } ], "_stars": 1, "_contributors": [ { "user": "nirmalaruban", "count": 3, "uuid": 199979695 } ], "_userbio": { "uuid": 199979695, "type": "user", "name": "Nirmalaruban", "followers": 1 }, "_downloads": { "count": 319, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/geneNR" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/geneNR.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_realowner": "nirmalaruban", "_cranurl": false, "_releases": [ { "version": "1.0.1", "date": "2025-03-10" }, { "version": "2.0.1", "date": "2025-03-29" }, { "version": "3.0.0", "date": "2026-07-05" } ], "_exports": [ "geneQTL", "geneSNP", "geneSNPcustom", "import_hmp", "import_vcf", "plot_SNP", "plot_summariseSNP", "summariseSNP", "summariseSNP_vcf" ], "_datasets": [ { "name": "sample_data_rice", "title": "Sample Data", "object": "sample_data_rice", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "traits", "SNP", "Chr", "Pos" ], "rows": 3, "table": true, "tojson": true }, { "name": "sample_data_rice_qtl", "title": "Sample Data", "object": "sample_data_rice_qtl", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "traits", "Chr", "start", "stop" ], "rows": 3, "table": true, "tojson": true }, { "name": "sample_data_wheat", "title": "Sample Data", "object": "sample_data_wheat", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "SNP", "Chr", "Pos", "traits" ], "rows": 3, "table": true, "tojson": true }, { "name": "sample_data_wheat_custom", "title": "Sample Data", "object": "sample_data_wheat_custom", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "traits", "SNP", "Chr", "start", "stop" ], "rows": 3, "table": true, "tojson": true }, { "name": "sample_data_wheat_qtl", "title": "Sample Data", "object": "sample_data_wheat_qtl", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "traits", "Chr", "start", "stop" ], "rows": 3, "table": true, "tojson": true } ], "_help": [ { "page": "geneQTL", "title": "Identifies Candidate Genes based on identified Quantitative Trait Loci (QTL) analysis", "topics": [ "geneQTL" ] }, { "page": "geneSNP", "title": "Identifies Candidate Genes based on identified Single Nucleotide Polymorphisms (SNPs) from Genome Wide Association Studies (GWAS) Analysis", "topics": [ "geneSNP" ] }, { "page": "geneSNPcustom", "title": "Identifies Candidate Genes based on identified Single Nucleotide Polymorphisms (SNPs) from Genome Wide Association Studies (GWAS) Analysis", "topics": [ "geneSNPcustom" ] }, { "page": "import_hmp", "title": "Imports Hapmap genotypic data file", "topics": [ "import_hmp" ] }, { "page": "import_vcf", "title": "Imports VCF (Variant Call Format) data file", "topics": [ "import_vcf" ] }, { "page": "plot_SNP", "title": "Plot SNP Distribution on Chromosome Map", "topics": [ "plot_SNP" ] }, { "page": "plot_summariseSNP", "title": "Plot SNP Distribution Across Chromosomes", "topics": [ "plot_summariseSNP" ] }, { "page": "sample_data_rice", "title": "Sample Data", "topics": [ "sample_data_rice" ] }, { "page": "sample_data_rice_qtl", "title": "Sample Data", "topics": [ "sample_data_rice_qtl" ] }, { "page": "sample_data_wheat", "title": "Sample Data", "topics": [ "sample_data_wheat" ] }, { "page": "sample_data_wheat_custom", "title": "Sample Data", "topics": [ "sample_data_wheat_custom" ] }, { "page": "sample_data_wheat_qtl", "title": "Sample Data", "topics": [ "sample_data_wheat_qtl" ] }, { "page": "summariseSNP", "title": "Distribution of SNPs Across Chromosomes", "topics": [ "summariseSNP" ] }, { "page": "summariseSNP_vcf", "title": "Distribution of SNPs Across Chromosomes from VCF", "topics": [ "summariseSNP_vcf" ] } ], "_rundeps": [ "ape", "askpass", "bit", "bit64", "cli", "clipr", "cluster", "cpp11", "crayon", "curl", "digest", "dplyr", "farver", "generics", "ggplot2", "ggrepel", "glue", "gtable", "hms", "httr", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memuse", "mgcv", "mime", "nlme", "openssl", "permute", "pillar", "pinfsc50", "pkgconfig", "prettyunits", "progress", "R6", "RColorBrewer", "Rcpp", "readr", "rlang", "rvest", "S7", "scales", "selectr", "stringi", "stringr", "sys", "tibble", "tidyselect", "tzdb", "utf8", "vcfR", "vctrs", "vegan", "viridisLite", "vroom", "withr", "writexl", "xml2" ], "_vignettes": [ { "source": "geneNR_1.Rmd", "filename": "geneNR_1.html", "title": "Introduction of 'geneNR'", "author": "Rajamani Nirmalaruban", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Key Features", "Technical Pipeline & Parameter Configurations", "Gene Mining Function Arguments", "Target Reference Genome Assemblies", "Step-by-Step Executions", "Workflow 1: Instant Local Tracking Engine (CRAN Safe)", "Workflow 2: Online Real-Time Web Scraping Mode", "Workflow 3: Custom Haplotype Range Testing (geneSNPcustom)", "Genomic Data Summarization & Visualization", "Parsing and Summarizing Genotypic Data", "Mapping Chromosomal Density Charts (plot_SNP)", "Visualizing Frequency Histograms (plot_summariseSNP)", "System Output Layout", "Support & Package Maintenance", "Glossary" ], "created": "2025-03-10 15:32:53", "modified": "2026-07-05 15:10:02", "commits": 3 } ], "_score": 2, "_indexed": true, "_nocasepkg": "genenr", "_universes": [ "nirmalaruban" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.0.0", "date": "2026-10-23T08:28:13.000Z", "distro": "resolute", "commit": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "fileid": "https://r2.ropensci.org/e8894e6badc07dce92d6d3d26ac334ab43a1ff871092757df1c1c14c72a542fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486" }, { "r": "4.6.1", "os": "linux", "version": "3.0.0", "date": "2026-10-23T08:28:02.000Z", "distro": "resolute", "commit": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "fileid": "https://r2.ropensci.org/e66790d4d82f3334083b0bf2dc24c8c309b8a150a3225e5536e019656c096428", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486" }, { "r": "4.5.3", "os": "mac", "version": "3.0.0", "date": "2026-10-23T08:28:51.000Z", "commit": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "fileid": "https://r2.ropensci.org/eee5075396a500eb0ee1b52439bc8b3b1cba79aa5cc277a9c49a5b4e57da1b78", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486" }, { "r": "4.6.1", "os": "mac", "version": "3.0.0", "date": "2026-10-23T08:28:37.000Z", "commit": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "fileid": "https://r2.ropensci.org/27e6a507d0c604fa0e8be1259aca8a7b79d893de73f41237f718f4efde0e4e1c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486" }, { "r": "4.6.0", "os": "wasm", "version": "3.0.0", "date": "2026-10-23T08:28:06.000Z", "commit": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "fileid": "https://r2.ropensci.org/eeb5e5325db9fdf8becea6c1a27b29eb060e27bbe2806347c056d8eaab566e9e", "status": "success", "buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486" }, { "r": "4.7.0", "os": "win", "version": "3.0.0", "date": "2026-10-23T08:27:08.000Z", "commit": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "fileid": "https://r2.ropensci.org/fe93833ff7c4181dee4fef43df45b151627a6e9617f338dc03b7c47ab2b9e93e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486" }, { "r": "4.5.3", "os": "win", "version": "3.0.0", "date": "2026-10-23T08:27:18.000Z", "commit": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "fileid": "https://r2.ropensci.org/8831b43ae3a01465d719ff0eefe2b56163e85b53511c5e4701b546d8532b4823", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486" }, { "r": "4.6.1", "os": "win", "version": "3.0.0", "date": "2026-10-23T08:27:21.000Z", "commit": "b34c8c709bdcd0b1d6a79b021985e568dd53eba6", "fileid": "https://r2.ropensci.org/6fcfe4f2105fe00ba88551fb53e63f08b974d415fe30c8f95a4024f9e4a498c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nirmalaruban/actions/runs/39923844486" } ] }