{ "_id": "6a1f2ab6b401979e73424b8d", "Package": "tidyGenR", "Title": "Tidy Multilocus Amplicon Genotypes", "Version": "0.1.8", "Authors@R": "c(\nperson(\"Miguel\", \"Camacho\", , \"miguelcamachosanchez@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-6385-7963\")),\nperson(\"Jennifer\", \"Leonard\", role = \"fnd\")\n)", "Description": "Variant determination and genotyping from high throughput\nsequences from multilocus amplicon libraries, typically\nsequenced in Illumina MiSeq or similar. It provides a set of\ncore functions for the central steps: demultiplex by locus,\ntruncate reads, variant calling, and genotype calling.\nAdditionally, it provides a set of functions for diagnosis and\nestimation of best running parameters and multiple extensions\nfor genotype/variants manipulation and reformatting. Output\nvariants and genotypes are output in 'tidy' format, thus\nfacilitating reformatting, manipulation and potential\nconnection to other R packages.", "License": "GPL (>= 3)", "URL": "https://github.com/csmiguel/tidyGenR", "BugReports": "https://github.com/csmiguel/tidyGenR/issues", "biocViews": "Software, Sequencing, Classification, Phylogenetics", "Encoding": "UTF-8", "LazyData": "false", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 12:28:23 UTC", "User": "root" }, "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "SystemRequirements": "cutadapt >=2.0\n(https://cutadapt.readthedocs.io/en/stable/)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://csmiguel.r-universe.dev", "Date/Publication": "2026-05-15 10:59:16 UTC", "RemoteUrl": "https://github.com/csmiguel/tidygenr", "RemoteRef": "HEAD", "RemoteSha": "c8f9e1eae7b105dd30fb2987897a2b25f2994180", "Author": "Miguel Camacho [aut, cre, cph] (ORCID:\n),\nJennifer Leonard [fnd]", "Maintainer": "Miguel Camacho ", "MD5sum": "852650beb824770577fc2792786f00e7", "_user": "csmiguel", "_type": "src", "_file": "tidyGenR_0.1.8.tar.gz", "_fileid": "6353726909888888872c18955132d1294d5fcf9a0392511ad3406fd50d3141a1", "_filesize": 1425459, "_sha256": "6353726909888888872c18955132d1294d5fcf9a0392511ad3406fd50d3141a1", "_created": "2026-05-15T12:28:23.000Z", "_published": "2026-06-02T19:10:46.178Z", "_distro": "noble", "_jobs": [ { "job": 79151145001, "time": 390, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7017155823" }, { "job": 79151144900, "time": 419, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7017163996" }, { "job": 79151145076, "time": 293, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7017122573" }, { "job": 79151144892, "time": 339, "config": 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}, { "page": "check_raw_reads", "title": "Check input raw FASTA/Q files", "topics": [ "check_raw_reads" ] }, { "page": "check1_lowcount", "title": "Check1", "topics": [ "check1_lowcount" ] }, { "page": "check2_unique_snames", "title": "Check2", "topics": [ "check2_unique_snames" ] }, { "page": "check3_non_orphan", "title": "Check3", "topics": [ "check3_non_orphan" ] }, { "page": "compare_calls", "title": "Comparision between multiple tidy variants or genotypes.", "topics": [ "compare_calls" ] }, { "page": "cutadapt_command", "title": "Create cutadapt command", "topics": [ "cutadapt_command" ] }, { "page": "demultiplex", "title": "Demultiplex reads by locus", "topics": [ "demultiplex" ] }, { "page": "dereplicate", "title": "De-replicate reads into frequency tables for a set of FASTQ files", "topics": [ "dereplicate" ] }, { "page": "dist_m", "title": "Distance between two matrices", "topics": [ "dist_m" ] }, { "page": "dist_m_all", "title": "Applies distance between all tables in a 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