{ "_id": "6ac78dc7de46216d5edd2225", "Package": "findGSEP", "Type": "Package", "Title": "Estimate Genome Size of Polyploid Species Using k-Mer\nFrequencies", "Version": "1.2.0", "Authors@R": "c(\nperson(\"Laiyi\", \"Fu\", role = c(\"aut\", \"cre\"), email = \"fulaiyi321@163.com\"),\nperson(\"Hequan\", \"Sun\", role = \"aut\"))", "Maintainer": "Laiyi Fu ", "Description": "Provides tools to estimate the genome size of polyploid\nspecies using k-mer frequencies. This package includes\nfunctions to process k-mer frequency data and perform genome\nsize estimation by fitting k-mer frequencies with a normal\ndistribution model. It supports handling of complex polyploid\ngenomes and offers various options for customizing the\nestimation process. The basic method 'findGSE' is detailed in\nSun, Hequan, et al. (2018) .", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "URL": "https://github.com/sperfu/findGSEP", "BugReports": "https://github.com/sperfu/findGSEP/issues", "VignetteBuilder": "knitr", "Repository": "https://sperfu.r-universe.dev", "Date/Publication": "2024-07-27 03:03:15 UTC", "RemoteUrl": "https://github.com/sperfu/findgsep", "RemoteRef": "HEAD", "RemoteSha": "8bef3bcce7d9b64e5ae287678ce2699576713281", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 12:29:22 UTC", "User": "root" }, "Author": "Laiyi Fu [aut, cre],\nHequan Sun [aut]", "_user": "sperfu", "_type": "src", "_file": "findGSEP_1.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/f7d45a0470c230fe576048376a38f4cdcbccad639497c1b4a81b3327b67bb2ba", "_filesize": 212327, "_sha256": "f7d45a0470c230fe576048376a38f4cdcbccad639497c1b4a81b3327b67bb2ba", "_expires": "2027-01-16T12:34:12.000Z", "_created": "2026-10-08T12:29:22.000Z", "_published": "2026-10-08T12:34:15.028Z", "_buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113311135567, "time": 121, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11550845666" }, { "job": 113311135600, "time": 110, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11550795611" }, { "job": 113311135593, "time": 100, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11551145515" }, { "job": 113311135575, "time": 116, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11550880990" }, { "job": 113310007094, "time": 167, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11551115222" }, { "job": 113311135744, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11551170487" }, { "job": 113311135725, "time": 89, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11551385276" }, { "job": 113311135824, "time": 104, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11550840666" }, { "job": 113311135682, "time": 94, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11551140354" } ], "_upstream": "https://github.com/sperfu/findgsep", "_commit": { "id": "8bef3bcce7d9b64e5ae287678ce2699576713281", "author": "Laiyi Fu ", "committer": "GitHub ", "message": "Update README.md", "time": 1722049395 }, "_maintainer": { "name": "Laiyi Fu", "email": "fulaiyi321@163.com", "login": "sperfu", "description": "Interested in Computation Biology and Bioinformatics.", "uuid": 19401324 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "RColorBrewer", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "grDevices", "role": "Depends" }, { "package": "pracma", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "sperfu", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 10, "_contributors": [ { "user": "sperfu", "count": 32, "uuid": 19401324 } ], "_userbio": { "uuid": 19401324, "type": "user", "name": "Laiyi Fu", "followers": 18, "description": "Interested in Computation Biology and Bioinformatics." }, "_downloads": { "count": 313, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/findGSEP" }, "_devurl": "https://github.com/sperfu/findgsep", "_searchresults": 3, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/findGSEP.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/sperfu/findgsep", "_realowner": "sperfu", "_cranurl": true, "_releases": [ { "version": "1.2.0", "date": "2024-05-26" } ], "_exports": [ "error_minimize", "error_minimize_raw", "error_minimize2", "error_minimize2_raw", "error_minimize3", "error_minimize3_raw", "filter_peaks", "filter_peaks_raw", "findGSE_raw", "findGSE_sp", "findGSEP", "get_het_pos", "initial_count_recover", "initial_count_recover_raw", "initialize_start_time", "kmer_count_modify", "kmer_count_modify_raw" ], "_help": [ { "page": "error_minimize", "title": "Minimize the Error for K-mer Frequency Fitting", "topics": [ "error_minimize" ] }, { "page": "error_minimize_raw", "title": "Minimize the Error for Raw K-mer Frequency Fitting", "topics": [ "error_minimize_raw" ] }, { "page": "error_minimize2", "title": "Tuning Final Fitting for Heterozygous Genomes", "topics": [ "error_minimize2" ] }, { "page": "error_minimize2_raw", "title": "Tuning Final Fitting for Raw Heterozygous Genomes", "topics": [ "error_minimize2_raw" ] }, { "page": "error_minimize3", "title": "Minimize the Error for Remaining K-mer Frequency", "topics": [ "error_minimize3" ] }, { "page": "error_minimize3_raw", "title": "Minimize the Error for Raw Remaining K-mer Frequency", "topics": [ "error_minimize3_raw" ] }, { "page": "filter_peaks", "title": "Filter Peaks from K-mer Histogram", "topics": [ "filter_peaks" ] }, { "page": "filter_peaks_raw", "title": "Filter Peaks from Raw K-mer Histogram", "topics": [ "filter_peaks_raw" ] }, { "page": "findGSE_raw", "title": "Estimate Genome Size Using Raw K-mer Frequencies", "topics": [ "findGSE_raw" ] }, { "page": "findGSE_sp", "title": "Estimate Genome Size Using K-mer Frequencies", "topics": [ "findGSE_sp" ] }, { "page": "findGSEP", "title": "Estimate genome size of polyploid species using k-mer frequencies.", "topics": [ "findGSEP" ] }, { "page": "get_het_pos", "title": "Filter Peaks from K-mer Histogram", "topics": [ "get_het_pos" ] }, { "page": "initial_count_recover", "title": "Recover Initial K-mer Count", "topics": [ "initial_count_recover" ] }, { "page": "initial_count_recover_raw", "title": "Recover Initial Raw K-mer Count", "topics": [ "initial_count_recover_raw" ] }, { "page": "initialize_start_time", "title": "Initialize Start Time", "topics": [ "initialize_start_time" ] }, { "page": "kmer_count_modify", "title": "Modify K-mer Frequency Before Fitting", "topics": [ "kmer_count_modify" ] }, { "page": "kmer_count_modify_raw", "title": "Modify Raw K-mer Frequency Before Fitting", "topics": [ "kmer_count_modify_raw" ] } ], "_readme": "https://github.com/sperfu/findgsep/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "pillar", "pkgconfig", "pracma", "R6", "RColorBrewer", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "vignette.Rmd", "filename": "vignette.html", "title": "vignette", "engine": "knitr::rmarkdown", "headings": [ "title: \"Estimate Genome Size of Polyploid Species Using K-mer Frequencies\"output: html_document", "Description", "Usage", "Arguments", "Example Usage", "References", "Session Info" ], "created": "2024-05-15 09:47:09", "modified": "2024-05-22 01:32:19", "commits": 3 } ], "_score": 4.698970004336019, "_indexed": true, "_nocasepkg": "findgsep", "_universes": [ "sperfu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.0", "date": "2026-10-08T12:31:15.000Z", "distro": "resolute", "commit": "8bef3bcce7d9b64e5ae287678ce2699576713281", "fileid": "https://r2.ropensci.org/9b2bde312d524368f829ffc830baf4694fa406aed71af300afc9a5d7c3864af6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226" }, { "r": "4.6.1", "os": "linux", "version": "1.2.0", "date": "2026-10-08T12:31:08.000Z", "distro": "resolute", "commit": "8bef3bcce7d9b64e5ae287678ce2699576713281", "fileid": "https://r2.ropensci.org/9d361c7cfe01e6531e0fd53254f8adcb8285c86d1f15d925a4d56a6f0c6c751f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226" }, { "r": "4.5.3", "os": "mac", "version": "1.2.0", "date": "2026-10-08T12:31:58.000Z", "commit": "8bef3bcce7d9b64e5ae287678ce2699576713281", "fileid": "https://r2.ropensci.org/6c41a481be062f162c9f26fdc1156fffe54cb907f12c7cde3f5ae49bb061a283", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226" }, { "r": "4.6.1", "os": "mac", "version": "1.2.0", "date": "2026-10-08T12:33:07.000Z", "commit": "8bef3bcce7d9b64e5ae287678ce2699576713281", "fileid": "https://r2.ropensci.org/c52fde2e029408886c60f1197d34ac97e4f4d8bfe6db5b95c83774b8bd9ae809", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.0", "date": "2026-10-08T12:31:39.000Z", "commit": "8bef3bcce7d9b64e5ae287678ce2699576713281", "fileid": "https://r2.ropensci.org/72c31e1f8e2bc402a3d8135347b6120b33b0e4616536f8f443e6e7330e2f6dd1", "status": "success", "buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226" }, { "r": "4.7.0", "os": "win", "version": "1.2.0", "date": "2026-10-08T12:30:36.000Z", "commit": "8bef3bcce7d9b64e5ae287678ce2699576713281", "fileid": "https://r2.ropensci.org/8cf8db8f9539b7551f5493d35a28d3bd8a52545db64033cf1b08b17ba310c052", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226" }, { "r": "4.5.3", "os": "win", "version": "1.2.0", "date": "2026-10-08T12:30:56.000Z", "commit": "8bef3bcce7d9b64e5ae287678ce2699576713281", "fileid": "https://r2.ropensci.org/6b1cca7f93df6d8d08208ed56dddbf282deea5fa37fd40a7d13c89a6babc7ec1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226" }, { "r": "4.6.1", "os": "win", "version": "1.2.0", "date": "2026-10-08T12:30:43.000Z", "commit": "8bef3bcce7d9b64e5ae287678ce2699576713281", "fileid": "https://r2.ropensci.org/637a95718beee61fec8797ce9360925182dfd47d83b8b38c5faf9c3f2def1744", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/sperfu/actions/runs/37776876226" } ] }