{ "_id": "6a624f3b717f18b497d418a7", "Package": "rchime", "Type": "Package", "Title": "Detect and Remove Chimeras from Amplicon Sequence Analysis Data", "Version": "0.1.0", "Date": "2026-07-07", "Authors@R": "c(\nperson(\"Sarah\", \"Westcott\", , \"swestcot@umich.edu\", role = c(\"aut\"),\ncomment = c(ORCID = \"0009-0001-1529-8247\")),\nperson(\"Pat\", \"Schloss\", , \"pschloss@umich.edu\", role = c(\"cph\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6935-4275\")),\nperson(\"Torbjorn\", \"Rognes\", , \"torognes@ifi.uio.no\", role = c(\"cph\")),\nperson(\"Frederic\", \"Mahe\", , \"mahe@rhrk.uni-kl.de\", role = c(\"cph\")),\nperson(\"Tomas\", \"Flouri\", , \"tomas.flouri@h-its.org\", role = c(\"cph\")),\nperson(\"Christopher\", \"Quince\", , \"c.quince@warwick.ac.uk\", role = c(\"cph\")),\nperson(\"Ben\", \"Nichols\", , \"b.nichols.1@research.gla.ac.uk\", role = c(\"cph\")))", "Maintainer": "Pat Schloss ", "Description": "Detect and remove chimeras from your amplicon sequence\nanalysis using reference-based or de novo approaches. The\n'rchime' package implements the 'VSEARCH' algorithms described\nin Rognes et al. (2016) . 'VSEARCH'\nbuilds on the work of Edgar,R.C. et al. (2011)\n.", "URL": "https://github.com/mothur/rchime, https://mothur.org/rchime/", "BugReports": "https://github.com/mothur/rchime/issues", "License": "GPL (>= 3)", "Config/testthat/edition": "3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-23 17:14:49 UTC", "User": "root" }, "Author": "Sarah Westcott [aut] (ORCID:\n), Pat Schloss [cph,\ncre] (ORCID: ), Torbjorn\nRognes [cph], Frederic Mahe [cph], Tomas Flouri [cph],\nChristopher Quince [cph], Ben Nichols [cph]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-07-23 14:20:02 UTC", "RemoteUrl": "https://github.com/cran/rchime", "RemoteRef": "HEAD", "RemoteSha": "5bb9e1c29e4e11f0ac7fd041d2b5f4ca1224d55a", "_user": "cran", "_type": "src", "_file": "rchime_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/9ad0f228ffa94506146fb067646ebaf79d61323ad831dd993106e5c6e17ab97c", "_filesize": 4235553, "_sha256": "9ad0f228ffa94506146fb067646ebaf79d61323ad831dd993106e5c6e17ab97c", "_expires": "2026-10-31T17:28:25.000Z", "_created": "2026-07-23T17:14:49.000Z", "_published": "2026-07-23T17:28:27.870Z", "_jobs": [ { "job": 89279447949, "time": 211, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8572603680" }, { "job": 89279447919, "time": 254, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8572621648" }, { "job": 89279447960, "time": 217, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8572604466" }, { "job": 89279447994, "time": 252, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8572620645" }, { "job": 89278008298, "time": 360, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8572339774" }, { "job": 89279447970, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 89279448017, "time": 428, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8572539246" }, { "job": 89279447955, "time": 226, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8572589951" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/30028211476", "_status": "success", "_upstream": "https://github.com/cran/rchime", "_commit": { "id": "5bb9e1c29e4e11f0ac7fd041d2b5f4ca1224d55a", "author": "Pat Schloss ", "committer": "cran-robot ", "message": "version 0.1.0\n", "time": 1784816402 }, "_maintainer": { "name": "Pat Schloss", "email": "pschloss@umich.edu", "login": "pschloss", "orcid": "0000-0002-6935-4275", "description": "A microbiologist at the University of Michigan. ORCID: 0000-0002-6935-4275. Runner of https://github.com/SchlossLab", "uuid": 1264132 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "Depends" }, { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "strollur", "version": ">= 0.1.3", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppThread", "role": "LinkingTo" }, { "package": "RcppXsimd", "role": "LinkingTo" }, { "package": "cli", "role": "LinkingTo" }, { "package": "cli", "role": "Imports" }, { "package": "parallelly", "role": "Imports" }, { "package": "RcppThread", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" }, { "package": "pak", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-30", "n": 1 } ], "_tags": [ { "name": "0.1.0", "date": "2026-07-23" } ], "_stars": 0, "_contributors": [ { "user": "pschloss", "count": 1, "uuid": 1264132 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 623, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rchime" }, "_devurl": "https://github.com/mothur/rchime", "_pkgdown": "https://mothur.org/rchime/", "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/rchime.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2026-07-23" } ], "_exports": [ "rchime", "rchime_example", "rchime_options", "silva_gold" ], "_help": [ { "page": "rchime", "title": "Detect and remove chimeras from your strollur object or data.frame using a de novo approach or alternatively a reference model.", "topics": [ "rchime" ] }, { "page": "rchime_example", "title": "Get path to rchime example files", "topics": [ "rchime_example" ] }, { "page": "rchime_options", "title": "The 'rchime_options()' function allows you to set vsearch specific optional parameters.", "topics": [ "rchime_options" ] }, { "page": "rchime.data.frame", "title": "Detect chimeras in your data.frames.", "topics": [ "rchime.data.frame" ] }, { "page": "rchime.strollur", "title": "Detect and remove chimeras from your strollur dataset object.", "topics": [ "rchime.strollur" ] }, { "page": "silva_gold", "title": "silva_gold", "topics": [ "silva_gold" ] } ], "_pkglogo": "https://github.com/cran/rchime/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/cran/rchime/raw/HEAD/README.md", "_rundeps": [ "ape", "beeswarm", "bit", "bit64", "cellranger", "cli", "clipr", "cluster", "commonmark", "cpp11", "crayon", "curl", "data.table", "diffobj", "digest", "dplyr", "ecodive", "emmeans", "estimability", "farver", "fillpattern", "generics", "ggbeeswarm", "ggnewscale", "ggplot2", "ggrepel", "ggtext", "glue", "gridtext", "gtable", "hms", "isoband", "jpeg", "jsonlite", "labeling", "lattice", "lifecycle", "litedown", "magrittr", "markdown", "MASS", "Matrix", "mgcv", "microseq", "mvtnorm", "nlme", "numDeriv", "parallelly", "patchwork", "permute", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rbiom", "Rcereal", "RColorBrewer", "Rcpp", "RcppThread", "RcppXsimd", "readr", "readxl", "rematch", "rlang", "S7", "scales", "stringi", "stringr", "strollur", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "vegan", "vipor", "viridisLite", "vroom", "waldo", "withr", "xfun", "xml2", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "chimera_report.Rmd", "filename": "chimera_report.html", "title": "chimera_report", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Example" ], "created": "2026-07-23 14:20:02", "modified": "2026-07-23 14:20:02", "commits": 1 }, { "source": "denovo_based_detection.Rmd", "filename": "denovo_based_detection.html", "title": "De novo Chimera Detection", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Creating strollur objects", "Loading data.frames", "Removing chimeras", "Results", "Chimera Report", "Chimeras", "Set_abundance_values" ], "created": "2026-07-23 14:20:02", "modified": "2026-07-23 14:20:02", "commits": 1 }, { "source": "rchime.Rmd", "filename": "rchime.html", "title": "Getting Started", "engine": "knitr::rmarkdown", "headings": [ "Installing rchime", "Tutorials to help you get started" ], "created": "2026-07-23 14:20:02", "modified": "2026-07-23 14:20:02", "commits": 1 }, { "source": "reference_based_detection.Rmd", "filename": "reference_based_detection.html", "title": "Reference Based Chimera Detection", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Creating strollur objects", "Loading data.frames", "Removing chimeras", "Results", "Chimera Report", "Chimeras" ], "created": "2026-07-23 14:20:02", "modified": "2026-07-23 14:20:02", "commits": 1 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "rchime", "_universes": [ "cran", "pschloss", "mothur" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-07-23T17:23:42.000Z", "distro": "resolute", "arch": "aarch64", "commit": "5bb9e1c29e4e11f0ac7fd041d2b5f4ca1224d55a", "fileid": "https://r2.ropensci.org/f5918ef4788b72793fc63e7933906b5cd9fe739123914b9ad8cd4f4ce6da8bd9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30028211476" }, { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-07-23T17:24:02.000Z", "distro": "resolute", "arch": "x86_64", "commit": "5bb9e1c29e4e11f0ac7fd041d2b5f4ca1224d55a", "fileid": "https://r2.ropensci.org/989a1a5398dc8f42bdf1d282d3cac150c37e63257a0392135ea643bb23198906", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30028211476" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-07-23T17:23:42.000Z", "distro": "resolute", "arch": "aarch64", "commit": "5bb9e1c29e4e11f0ac7fd041d2b5f4ca1224d55a", "fileid": "https://r2.ropensci.org/8abe2eff140aedf246d576129e29d45111fa0e296acd1e0830cc2d6f11b15628", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30028211476" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-07-23T17:23:58.000Z", "distro": "resolute", "arch": "x86_64", "commit": "5bb9e1c29e4e11f0ac7fd041d2b5f4ca1224d55a", "fileid": "https://r2.ropensci.org/4719cb7657f69d38809e5799c3072e22cd72adc9213a2f3da57e4c8bc48c2af3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30028211476" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-07-23T17:20:26.000Z", "arch": "aarch64", "commit": "5bb9e1c29e4e11f0ac7fd041d2b5f4ca1224d55a", "fileid": "https://r2.ropensci.org/7dd793a6f290116b0d54c02a468f2f2a188def9a873a19f56a895aa72131f64e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30028211476" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-07-23T17:22:22.000Z", "arch": "x86_64", "commit": "5bb9e1c29e4e11f0ac7fd041d2b5f4ca1224d55a", "fileid": "https://r2.ropensci.org/98d6aa2948242580aa508def3db5145408b959ffafd652858e8ae189e39e51f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/30028211476" } ] }