{ "_id": "6a213f89cd65a98ecbd29f28", "Package": "GARCOM", "Type": "Package", "Title": "Gene and Region Counting of Mutations (\"GARCOM\")", "Version": "1.2.2", "Authors@R": "c(person(\"Sanjeev\",\"Sariya\",\nrole = c(\"aut\", \"cre\",\"cph\"),email = \"sanjeevsariya@gmail.com\"),person(\"Giuseppe\",\"Tosto\", role =c(\"aut\",\"cph\")))", "Description": "Gene and Region Counting of Mutations (GARCOM) package\ncomputes mutation (or alleles) counts per gene per individuals\nbased on gene annotation or genomic base pair boundaries. It\ncomes with features to accept data formats in plink(.raw) and\nVCF. It provides users flexibility to extract and filter\nindividuals, mutations and genes of interest.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://complexgenome.r-universe.dev", "Date/Publication": "2022-12-23 11:37:19 UTC", "RemoteUrl": "https://github.com/complexgenome/garcom", "RemoteRef": "HEAD", "RemoteSha": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 09:00:14 UTC", "User": "root" }, "Author": "Sanjeev Sariya [aut, cre, cph],\nGiuseppe Tosto [aut, cph]", "Maintainer": "Sanjeev Sariya ", "MD5sum": "a571a4a0affa574b7534aa287e52fd0d", "_user": "complexgenome", "_type": "src", "_file": "GARCOM_1.2.2.tar.gz", "_fileid": "d60f28dbc03f631fdef390be345a27705d15fc6e87d7bf5c7aa879f5d64ddeaf", "_filesize": 129416, "_sha256": "d60f28dbc03f631fdef390be345a27705d15fc6e87d7bf5c7aa879f5d64ddeaf", "_created": "2026-06-04T09:00:14.000Z", "_published": "2026-06-04T09:04:09.865Z", "_distro": "noble", "_jobs": [ { "job": 79485080879, "time": 139, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7407350701" }, { "job": 79485080862, "time": 158, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7407357164" }, { "job": 79485080847, "time": 154, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7407346848" }, { "job": 79485080956, "time": 182, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7407354327" }, { "job": 79484614629, "time": 167, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7407302133" }, { "job": 79485080827, "time": 123, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7407345516" }, { "job": 79485080920, "time": 94, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7407335008" }, { "job": 79485080867, "time": 113, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7407341691" }, { "job": 79485080891, "time": 109, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7407340256" } ], "_buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/complexgenome/garcom", "_commit": { "id": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "author": "Sanjeev Sariya ", "committer": "Sanjeev Sariya ", "message": "put back data in vcf format as object stored\n", "time": 1671795439 }, "_maintainer": { "name": "Sanjeev Sariya", "email": "sanjeevsariya@gmail.com", "login": "complexgenome", "description": "", "uuid": 5683969 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "data.table", "version": ">= 1.12.8", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "vcfR", "version": ">= 1.12.0", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "complexgenome", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "genetics", "mutation" ], "_stars": 0, "_contributors": [ { "user": "complexgenome", "count": 316, "uuid": 5683969 } ], "_userbio": { "uuid": 5683969, "type": "user", "name": "Sanjeev" }, "_downloads": { "count": 118, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GARCOM" }, "_devurl": "https://github.com/complexgenome/garcom", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GARCOM.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/complexgenome/garcom", "_realowner": "complexgenome", "_cranurl": true, "_releases": [ { "version": "1.2.0", "date": "2020-10-16" }, { "version": "1.2.1", "date": "2022-12-14" }, { "version": "1.2.2", "date": "2022-12-23" } ], "_exports": [ "gene_annot_counts", "gene_pos_counts", "vcf_counts_annot", "vcf_counts_SNP_genecoords" ], "_datasets": [ { "name": "genecoord", "title": "genecoord", "object": "genecoord", "class": [ "data.frame" ], "fields": [ "GENE", "START", "END" ], "rows": 5, "table": true, "tojson": true }, { "name": "recodedgen", "title": "recodedgen", "object": "recodedgen", "class": [ "data.frame" ], "fields": [ "FID", "IID", "PAT", "MAT", "SEX", "PHENOTYPE", "SNP1_A", "SNP2_T", "SNP3_G", "SNP4_C", "SNP5_C", "SNP6_G", "SNP7_G", "SNP8_C", "SNP9_T", "SNP10_A" ], "rows": 10, "table": true, "tojson": true }, { "name": "sample_chr21_vcf", "title": "sample_chr21_vcf", "object": "sample_chr21_vcf", "class": [ "vcfR" ], "fields": [], "table": false, "tojson": false }, { "name": "snpgene", "title": "snpgene", "object": "snpgene", "class": [ "data.frame" ], "fields": [ "GENE", "SNP" ], "rows": 10, "table": true, "tojson": true }, { "name": "snppos", "title": "snppos", "object": "snppos", "class": [ "data.frame" ], "fields": [ "SNP", "BP" ], "rows": 10, "table": true, "tojson": true } ], "_help": [ { "page": "gene_annot_counts", "title": "gene annotation counts", "topics": [ "gene_annot_counts" ] }, { "page": "gene_pos_counts", "title": "gene position counts", "topics": [ "gene_pos_counts" ] }, { "page": "genecoord", "title": "genecoord", "topics": [ "genecoord" ] }, { "page": "recodedgen", "title": "recodedgen", "topics": [ "recodedgen" ] }, { "page": "sample_chr21_vcf", "title": "sample_chr21_vcf", "topics": [ "sample_chr21_vcf" ] }, { "page": "snpgene", "title": "snpgene", "topics": [ "snpgene" ] }, { "page": "snppos", "title": "snppos", "topics": [ "snppos" ] }, { "page": "vcf_counts_annot", "title": "gene annotation counts using VCF data", "topics": [ "vcf_counts_annot" ] }, { "page": "vcf_counts_SNP_genecoords", "title": "VCF gene position counts", "topics": [ "vcf_counts_SNP_genecoords" ] } ], "_readme": "https://github.com/complexgenome/garcom/raw/HEAD/README.md", "_rundeps": [ "ape", "cli", "cluster", "data.table", "digest", "dplyr", "generics", "glue", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memuse", "mgcv", "nlme", "permute", "pillar", "pinfsc50", "pkgconfig", "R6", "Rcpp", "rlang", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vcfR", "vctrs", "vegan", "viridisLite", "withr" ], "_score": 2.6989700043360187, "_indexed": true, "_nocasepkg": "garcom", "_universes": [ "complexgenome" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.2", "date": "2026-06-04T09:02:21.000Z", "distro": "noble", "commit": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "fileid": "3c26a9823ba1fb868dd40dbfa7af8eb555c969e703124ff267965b890f3d0979", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127" }, { "r": "4.6.0", "os": "linux", "version": "1.2.2", "date": "2026-06-04T09:02:41.000Z", "distro": "noble", "commit": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "fileid": "006aaec2ef11cdb7b90e192a242cc25f7510e3487005544b0f4658ec5e2d6579", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127" }, { "r": "4.5.3", "os": "mac", "version": "1.2.2", "date": "2026-06-04T09:02:25.000Z", "commit": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "fileid": "ecde2c8c1bdc00c1142b27000b7992b227552bd1582839d78565803a9920dbd8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127" }, { "r": "4.6.0", "os": "mac", "version": "1.2.2", "date": "2026-06-04T09:02:31.000Z", "commit": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "fileid": "d84e1040dba232ee0770b2be806af8e542f6ced0ed860cf27cc2f5a60b233c1a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.2", "date": "2026-06-04T09:02:39.000Z", "commit": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "fileid": "6a93058fbe06e5c4db303e7c5775bf0cc4ccf16aeaa29c419eef10efb61ec6ea", "status": "success", "buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127" }, { "r": "4.7.0", "os": "win", "version": "1.2.2", "date": "2026-06-04T09:01:33.000Z", "commit": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "fileid": "5d4c9d1e0f21992ded45a6ccc2d4210a3b4ce9bc7bae6fc068fdf1e456841632", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127" }, { "r": "4.5.3", "os": "win", "version": "1.2.2", "date": "2026-06-04T09:01:44.000Z", "commit": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "fileid": "36c1b88c9987d09ac77f469c01c3419e786d8ba4b7e75d9792b6fea311bc735a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127" }, { "r": "4.6.0", "os": "win", "version": "1.2.2", "date": "2026-06-04T09:01:52.000Z", "commit": "53ad17a654c71ddbc6aacbf9065d2b736c3855fd", "fileid": "5cef449182ca6c36c22fccb3cac59aa78de370b2a996d6a73c6cd0c9277a32fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/complexgenome/actions/runs/26941700127" } ] }