{ "_id": "6a102deaacfb0bcc41c94081", "Package": "LorMe", "Title": "Lightweight One-Line Resolving Microbial Ecology Program", "Version": "2.0.2", "Authors@R": "c(person(given = \"Ningqi\",\nfamily = \"Wang\",\nrole = c(\"aut\", \"cre\",\"cph\"),\nemail = \"2434066068@qq.com\",),\nperson(given = \"Yaozhong\",\nfamily = \"Zhang\",\nrole = c(\"aut\"),\nemail = \"18888198926@163.com\",),\nperson(given = \"Gaofei\",\nfamily = \"Jiang\",\nrole = c(\"aut\"),\nemail = \"gjiang@njau.edu.cn\",))", "Maintainer": "Ningqi Wang <2434066068@qq.com>", "Description": "Provides a robust collection of functions tailored for\nmicrobial ecology analysis, encompassing both data analysis and\nvisualization. It introduces an encapsulation feature that\nstreamlines the process into a summary object. With the initial\nconfiguration of this summary object, users can execute a wide\nrange of analyses with a single line of code, requiring only\ntwo essential parameters for setup. The package delivers\ncomprehensive outputs including analysis objects, statistical\noutcomes, and visualization-ready data, enhancing the\nefficiency of research workflows. Designed with\nuser-friendliness in mind, it caters to both novices and\nseasoned researchers, offering an intuitive interface coupled\nwith adaptable customization options to meet diverse analytical\nneeds.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake libglpk-dev libgmp3-dev make libicu-dev\nlibjpeg-dev libpng-dev libuv1-dev libxml2-dev libmpfr-dev\nlibssl-dev libx11-dev zlib1g-dev", "Repository": "https://wangnq111.r-universe.dev", "Date/Publication": "2026-01-13 01:29:11 UTC", "RemoteUrl": "https://github.com/wangnq111/lorme", "RemoteRef": "HEAD", "RemoteSha": "2485eaee1b58e4597e3ec1a172d2750610c1802a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-13 05:36:25 UTC", "User": "root" }, "Author": "Ningqi Wang [aut, cre, cph],\nYaozhong Zhang [aut],\nGaofei Jiang [aut]", "MD5sum": "a11e4fbbd501b55ca14ea331faf05c77", "_user": "wangnq111", 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'getOption(\"LorMe\")' or 'LorMe_options()'", "topics": [ ".onLoad" ] }, { "page": "cash-LorMe-method", "title": "Access LorMe object elements via $", "topics": [ "$,LorMe-method" ] }, { "page": "add_tree", "title": "Attach phylogenetic tree to the LorMe object", "topics": [ "add_tree" ] }, { "page": "Alpha_diversity_calculator", "title": "Calculate alpha diversity based on tax summary object", "topics": [ "Alpha_diversity_calculator" ] }, { "page": "Alpha_diversity_calculator2", "title": "Calculate alpha diversity based on tax summary object or dataframe table", "topics": [ "Alpha_diversity_calculator2" ] }, { "page": "anova_report", "title": "Print Analysis of Variance report", "topics": [ "anova_report" ] }, { "page": "auto_signif_test", "title": "Automatic significance test", "topics": [ "auto_signif_test" ] }, { "page": "circulation_lm", "title": "Circulation of fitting Linear Models", "topics": [ "circulation_lm" ] }, { "page": "color_scheme", "title": "Get color scheme", "topics": [ "color_scheme" ] }, { "page": "combine_and_translate", "title": "Combine data for visualization", "topics": [ "combine_and_translate" ] }, { "page": "community_plot", "title": "Generate Community Composition Plot Based on Tax_summary Object", "topics": [ "community_plot" ] }, { "page": "compare_plot", "title": "Comparison plot generator This function help generate comparsion plot including bar plot, box plot, and violin plot", "topics": [ "compare_plot" ] }, { "page": "Deseq_analysis", "title": "Deseq Analysis Function", "topics": [ "Deseq_analysis" ] }, { "page": "Deseq_analysis2", "title": "Deseq analysis", "topics": [ "Deseq_analysis2" ] }, { "page": "differential_bar", "title": "Generate Differential Bar Plot and Error bar Plot", "topics": [ "differential_bar" ] }, { "page": "Dimension_reduction", "title": "Dimension_reduction: PCA, PCOA, and NMDS Analysis", "topics": [ "Dimension_reduction" ] }, { "page": "Facet_group", "title": "Tax summary object with Facet 2x2 Groups", "topics": [ "Facet_group" ] }, { "page": "Filter_function", "title": "Filter OTU/ASV/metagenomic profile/gene profile by threshold", "topics": [ "Filter_function" ] }, { "page": "indicator_analysis", "title": "Indicator Analysis", "topics": [ "indicator_analysis" ] }, { "page": "kruskal_report", "title": "Print Kruskal-Wallis Rank Sum Test report", "topics": [ "kruskal_report" ] }, { "page": "LorMe", "title": "LorMe package: Lightening One-Code Resolving Microbial Ecology Program", "topics": [ "LorMe" ] }, { "page": "LorMe_defaults", "title": "Restore LorMe global options to factory defaults", "topics": [ "LorMe_defaults" ] }, { "page": "LorMe_options", "title": "Change LorMe options", "topics": [ "LorMe_options" ] }, { "page": "LorMe_pipeline", "title": "One-stop microbial analysis pipeline for LorMe objects", "topics": [ "LorMe_pipeline" ] }, { "page": "LorMe-class", "title": "LorMe S4 class", "topics": [ "LorMe-class" ] }, { "page": "manhattan", "title": "Manhattan Plot 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