{ "_id": "6a104e80acfb0bcc41ca0ab6", "Package": "SQMtools", "Title": "Analyze Results Generated by the 'SqueezeMeta' Pipeline", "Version": "1.7.2", "Authors@R": "c( \nperson(\"Fernando\", \"Puente-Sánchez\", email = \"fernando.puente.sanchez@slu.se\", role = c(\"aut\", \"cre\")),\nperson(\"Natalia\", \"García-García\", email = \"ngarcia@cnb.csic.es\", role = c(\"aut\"))\n)", "Description": "'SqueezeMeta' is a versatile pipeline for the automated\nanalysis of metagenomics/metatranscriptomics data\n(). This package\nprovides functions loading 'SqueezeMeta' results into R,\nfiltering them based on different criteria, and visualizing the\nresults using basic plots. The 'SqueezeMeta' project (and any\nsubsets of it generated by the different filtering functions)\nis parsed into a single object, whose different components\n(e.g. tables with the taxonomic or functional composition\nacross samples, contig/gene abundance profiles) can be easily\nanalyzed using other R packages such as 'vegan' or 'DESeq2'.\nThe methods in this package are further described in\nPuente-Sánchez et al., (2020) .", "Author": "Fernando Puente-Sánchez [aut, cre], Natalia García-García [aut]", "Maintainer": "Fernando Puente-Sánchez ", "biocViews": "", "LazyDataCompression": "xz", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "BugReports": "https://github.com/jtamames/SqueezeMeta/issues", "URL": "https://github.com/jtamames/SqueezeMeta", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-10 06:16:15 UTC", "User": "root" }, "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-06-14 06:30:02 UTC", "RemoteUrl": "https://github.com/cran/SQMtools", "RemoteRef": "HEAD", "RemoteSha": "2facdf6b59349a77dafbb018e900fc291308e26e", "MD5sum": "4fe3cc5d34138889d26236013041a418", "_user": "cran", "_type": "src", "_file": "SQMtools_1.7.2.tar.gz", "_fileid": "a0b6d00f3bbe98c82f1f00261873082da449368db2f8c7c7338dbeaed1e440ca", "_filesize": 3546450, "_sha256": "a0b6d00f3bbe98c82f1f00261873082da449368db2f8c7c7338dbeaed1e440ca", "_created": "2026-05-10T06:16:15.000Z", "_published": "2026-05-22T12:39:28.094Z", "_distro": "noble", "_jobs": [ { "job": 77380944749, "time": 224, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6901538005" }, { "job": 77380944757, "time": 266, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6901541882" }, { "job": 77380944288, "time": 237, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6901516702" }, { "job": 77380944331, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160671112" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/25621500291", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/SQMtools", "_commit": { "id": "2facdf6b59349a77dafbb018e900fc291308e26e", "author": "Fernando Puente-Sánchez ", "committer": "cran-robot ", "message": "version 1.7.2\n", "time": 1749882602 }, "_maintainer": { "name": "Fernando Puente-Sánchez", "email": "fernando.puente.sanchez@slu.se" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "zip", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "pathview", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "vegan", "role": "Suggests" }, { "package": "microeco", "role": "Suggests" }, { "package": "phyloseq", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 1 }, { "week": "2025-24", "n": 1 } ], "_tags": [ { "name": "1.7.1", "date": "2025-06-04" }, { "name": "1.7.2", "date": "2025-06-14" } ], "_stars": 1, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 289, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SQMtools" }, "_devurl": "https://github.com/jtamames/squeezemeta", "_searchresults": 39, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/SQMtools.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.6.2", "date": "2023-03-20" }, { "version": "1.6.3", "date": "2023-09-18" }, { "version": "1.7.0", "date": "2025-03-31" }, { "version": "1.7.1", "date": "2025-06-04" }, { "version": "1.7.2", "date": "2025-06-14" } ], "_exports": [ "combineSQM", "combineSQMlite", "create_bin", "exportBins", "exportContigs", "exportKrona", "exportORFs", "exportPathway", "exportTable", "find_redundant_contigs", "loadSQM", "loadSQMlite", "mostAbundant", "mostVariable", "plotBars", "plotBins", "plotFunctions", "plotHeatmap", "plotTaxonomy", "remove_contigs_from_bin", "rowMaxs", "rowMins", "seqvec2fasta", "SQM_to_microeco", "SQM_to_phyloseq", "subsetBins", "subsetContigs", "subsetFun", "subsetORFs", "subsetRand", "subsetSamples", "subsetTax" ], "_datasets": [ { "name": "CheckMProkaryote", "title": "CheckM reference markers for Prokaryotes", "object": "CheckMProkaryote", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "Hadza", "title": "Hadza hunter-gatherer gut metagenomes", "object": "Hadza", "class": [ "SQM" ], "fields": [], "table": false, "tojson": false }, { "name": "MGKOs", "title": "Single Copy Phylogenetic Marker Genes from Sunagawa's group (KOs)", "object": "MGKOs", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "MGOGs", "title": "Single Copy Phylogenetic Marker Genes from Sunagawa's group (OGs)", "object": "MGOGs", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "RecA", "title": "RecA/RadA recombinase", "object": "RecA", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "USiCGs", "title": "Universal Single-Copy Genes", "object": "USiCGs", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "CheckMProkaryote", "title": "CheckM reference markers for Prokaryotes", "topics": [ "CheckMProkaryote" ] }, { "page": "combineSQM", "title": "Combine several SQM objects", "topics": [ "combineSQM" ] }, { "page": "combineSQMlite", "title": "Combine several SQM or SQMlite objects", "topics": [ "combineSQMlite" ] }, { "page": "create_bin", "title": "Create a bin from a vector of contigs", "topics": [ "create_bin" ] }, { "page": "exportBins", "title": "Export the bins of a SQM object", "topics": [ "exportBins" ] }, { "page": "exportContigs", "title": "Export the contigs of a SQM object", "topics": [ "exportContigs" ] }, { "page": "exportKrona", "title": "Export the taxonomy of a SQM object into a Krona Chart", "topics": [ "exportKrona" ] }, { "page": "exportORFs", "title": "Export the ORFs of a SQM object", "topics": [ "exportORFs" ] }, { "page": "exportPathway", "title": "Export the functions of a SQM object into KEGG pathway maps", "topics": [ "exportPathway" ] }, { "page": "exportTable", "title": "Export results in tabular format", "topics": [ "exportTable" ] }, { "page": "find_redundant_contigs", "title": "Find redundant contigs within a bin", "topics": [ "find_redundant_contigs" ] }, { "page": "Hadza", "title": "Hadza hunter-gatherer gut metagenomes", "topics": [ "Hadza" ] }, { "page": "loadSQM", "title": "Load a SqueezeMeta project into R", "topics": [ "loadSQM" ] }, { "page": "loadSQMlite", "title": "Load tables generated by 'sqm2tables.py', 'sqmreads2tables.py' or 'combine-sqm-tables.py' into R.", "topics": [ "loadSQMlite" ] }, { "page": "MGKOs", "title": "Single Copy Phylogenetic Marker Genes from Sunagawa's group (KOs)", "topics": [ "MGKOs" ] }, { "page": "MGOGs", "title": "Single Copy Phylogenetic Marker Genes from Sunagawa's group (OGs)", "topics": [ "MGOGs" ] }, { "page": "mostAbundant", "title": "Get the N most abundant rows (or columns) from a numeric table", "topics": [ "mostAbundant" ] }, { "page": "mostVariable", "title": "Get the N most variable rows (or columns) from a numeric table", "topics": [ "mostVariable" ] }, { "page": "plotBars", "title": "Plot a barplot using ggplot2", "topics": [ "plotBars" ] }, { "page": "plotBins", "title": "Barplot of the most abundant bins in a SQM object", "topics": [ "plotBins" ] }, { "page": "plotFunctions", "title": "Heatmap of the most abundant functions in a SQM object", "topics": [ "plotFunctions" ] }, { "page": "plotHeatmap", "title": "Plot a heatmap using ggplot2", "topics": [ "plotHeatmap" ] }, { "page": "plotTaxonomy", "title": "Barplot of the most abundant taxa in a SQM object", "topics": [ "plotTaxonomy" ] }, { "page": "RecA", "title": "RecA/RadA recombinase", "topics": [ "RecA" ] }, { "page": "remove_contigs_from_bin", "title": "Remove contigs from a given bin", "topics": [ "remove_contigs_from_bin" ] }, { "page": "rowMaxs", "title": "Return a vector with the row-wise maxima of a matrix or dataframe.", "topics": [ "rowMaxs" ] }, { "page": "rowMins", "title": "Return a vector with the row-wise minima of a matrix or dataframe.", "topics": [ "rowMins" ] }, { "page": "seqvec2fasta", "title": "Print a named vector of sequences as a fasta-formatted string", "topics": [ "seqvec2fasta" ] }, { "page": "SQM_to_microeco", "title": "Convert a SQM object into a microtable object from the _microeco_ package", "topics": [ "SQM_to_microeco" ] }, { "page": "SQM_to_phyloseq", "title": "Convert a SQM object into a phyloseq object from the _phyloseq_ package", "topics": [ "SQM_to_phyloseq" ] }, { "page": "subsetBins", "title": "Create a SQM object containing only the requested bins, and the contigs and ORFs contained in them.", "topics": [ "subsetBins" ] }, { "page": "subsetContigs", "title": "Select contigs", "topics": [ "subsetContigs" ] }, { "page": "subsetFun", "title": "Filter results by function", "topics": [ "subsetFun" ] }, { "page": "subsetORFs", "title": "Select ORFs", "topics": [ "subsetORFs" ] }, { "page": "subsetRand", "title": "Select random ORFs", "topics": [ "subsetRand" ] }, { "page": "subsetSamples", "title": "Filter results by sample", "topics": [ "subsetSamples" ] }, { "page": "subsetTax", "title": "Filter results by taxonomy", "topics": [ "subsetTax" ] }, { "page": "summary.SQM", "title": "summary method for class SQM", "topics": [ "summary.SQM" ] }, { "page": "summary.SQMbunch", "title": "summary method for class SQMbunch", "topics": [ "summary.SQMbunch" ] }, { "page": "summary.SQMlite", "title": "summary method for class SQMlite", "topics": [ "summary.SQMlite" ] }, { "page": "USiCGs", "title": "Universal Single-Copy Genes", "topics": [ "USiCGs" ] } ], "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "data.table", "DBI", "farver", "fastmap", "generics", "ggplot2", "glue", "graph", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGgraph", "KEGGREST", "labeling", "lifecycle", "magrittr", "memoise", "mime", "openssl", "org.Hs.eg.db", "pathview", "pkgconfig", "plyr", "png", "R6", "RColorBrewer", "Rcpp", "RCurl", "reshape2", "Rgraphviz", "rlang", "RSQLite", "S4Vectors", "S7", "scales", "Seqinfo", "stringi", "stringr", "sys", "vctrs", "viridisLite", "withr", "XML", "XVector", "zip" ], "_score": 1.8920946026904804, "_indexed": true, "_nocasepkg": "sqmtools", "_universes": [ "cran", "jtamames" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.2", "date": "2026-05-10T06:19:10.000Z", "distro": "noble", "commit": "2facdf6b59349a77dafbb018e900fc291308e26e", "fileid": "7069ec976e80f40ab10d55b5562fe299df172b19a54734bb8a796d3424f667aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25621500291" }, { "r": "4.6.0", "os": "linux", "version": "1.7.2", "date": "2026-05-10T06:19:48.000Z", "distro": "noble", "commit": "2facdf6b59349a77dafbb018e900fc291308e26e", "fileid": "492161aa3ee3ec242f4cb9b84ac1ce843d282b3462fcaff6473bf0bce2ca3cd8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25621500291" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.2", "date": "2026-05-22T12:39:01.000Z", "commit": "2facdf6b59349a77dafbb018e900fc291308e26e", "fileid": "fc9e32383b1b21df1a773366b4ac4b9781ee4db06ab0a5937071a1b671e69ed4", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25621500291" } ] }