{ "_id": "6a1edc2db401979e7340fc4d", "Package": "omu", "Title": "A Metabolomics Analysis Tool for Intuitive Figures and\nConvenient Metadata Collection", "Version": "1.1.0", "Authors@R": "person(\"Connor\", \"Tiffany\", email = \"crtiffany@ucdavis.edu\", role = c(\"aut\", \"cre\"))", "Description": "Facilitates the creation of intuitive figures to describe\nmetabolomics data by utilizing Kyoto Encyclopedia of Genes and\nGenomes (KEGG) hierarchy data, and gathers functional orthology\nand gene data from the KEGG-REST API.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.1", "VignetteBuilder": "knitr", "URL": "https://github.com/connor-reid-tiffany/Omu,\nhttps://www.kegg.jp/kegg/rest/keggapi.html", "BugReports": "https://github.com/connor-reid-tiffany/Omu/issues", "Config/pak/sysreqs": "cmake make libicu-dev libssl-dev", "Repository": "https://connor-reid-tiffany.r-universe.dev", "Date/Publication": "2023-10-15 17:35:27 UTC", "RemoteUrl": 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"_commit": { "id": "556731e5f7c027a6a4e7158a9b807680e5c860ec", "author": "Connor Tiffany ", "committer": "GitHub ", "message": "Merge pull request #20 from connor-reid-tiffany/KEGG_gather_update\n\nKegg gather update", "time": 1697391327 }, "_maintainer": { "name": "Connor Tiffany", "email": "crtiffany@ucdavis.edu", "login": "connor-reid-tiffany", "description": "", "uuid": 30420750 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "plyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "ggfortify", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "broom", "role": "Imports" }, { "package": "FSA", "role": "Imports" }, { "package": "rstatix", "role": "Imports" }, { "package": 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"version": "1.0.4", "date": "2020-05-18" }, { "version": "1.0.5", "date": "2022-05-25" }, { "version": "1.0.6", "date": "2022-06-10" }, { "version": "1.0.7", "date": "2022-08-27" }, { "version": "1.0.9", "date": "2023-02-02" }, { "version": "1.1.0", "date": "2023-04-06" }, { "version": "1.1.1", "date": "2023-10-17" }, { "version": "1.1.2", "date": "2024-03-07" } ], "_exports": [ "assign_hierarchy", "check_zeros", "count_fold_changes", "get_seqs", "KEGG_gather", "make_omelette", "omu_anova", "omu_summary", "PCA_plot", "pie_chart", "plate_omelette", "plate_omelette_rxnko", "plot_bar", "plot_boxplot", "plot_heatmap", "plot_rf_PCA", "plot_variable_importance", "plot_volcano", "ra_table", "random_forest", "read_metabo", "transform_metabolites", "transform_samples" ], "_datasets": [ { "name": "c57_nos2KO_mouse_countDF", "title": "c57b6J nos2KO metabolomics count matrix", "object": "c57_nos2KO_mouse_countDF", "class": [ "data.frame", "cpd" ], "fields": [ "Metabolite", "KEGG", "C289_1", "C289_2", "C289_3", "C289_4", "C290_1", "C290_2", "C291_1", "C291_2", "C296_1", "C296_2", "C297_1", "C297_2", "C298_1", "C298_2", "C299_1", "C299_2", "C300_1", "C300_2", "C301_1", "C301_2", "C290_3", "C290_4", "C291_3", "C291_4", "C298_3", "C298_4", "C299_3", "C299_4", "C300_3" ], "rows": 668, "table": true, "tojson": true }, { "name": "c57_nos2KO_mouse_metadata", "title": "c57b6J nos2KO meta data", "object": "c57_nos2KO_mouse_metadata", "class": [ "data.frame" ], "fields": [ "Sample", "Background", "Treatment", "Grouped" ], "rows": 29, "table": true, "tojson": true } ], "_help": [ { "page": "assign_hierarchy", "title": "Assign hierarchy metadata", "topics": [ "assign_hierarchy" ] }, { "page": "c57_nos2KO_mouse_countDF", "title": "c57b6J nos2KO metabolomics count matrix", "topics": [ "c57_nos2KO_mouse_countDF" ] }, { "page": "c57_nos2KO_mouse_metadata", "title": "c57b6J nos2KO meta data", "topics": [ "c57_nos2KO_mouse_metadata" ] }, { "page": "check_zeros", "title": "Check data for zeros across samples within factor levels. Will determine if there are more zeros than a user specified threshold within any given factor level(s). Returns a vector of Metabolites that are 0 above the threshold in any given factor level.", "topics": [ "check_zeros" ] }, { "page": "count_fold_changes", "title": "Get counts for significant fold changes by metabolite class.", "topics": [ "count_fold_changes" ] }, { "page": "get_seqs", "title": "Get nucleotide and amino acid sequences for genes", "topics": [ "get_seqs" ] }, { "page": "KEGG_gather", "title": "Gather metadata from KEGG for metabolites", "topics": [ "KEGG_gather", "KEGG_gather.cpd", "KEGG_gather.KO", "KEGG_gather.rxn" ] }, { "page": "make_omelette", "title": "Get metadata from KEGG API", "topics": [ "make_omelette" ] }, { "page": "omu_anova", "title": "Perform anova", "topics": [ "omu_anova" ] }, { "page": "omu_summary", "title": "omu_summary Performs comparison of means between two independent variables, standard deviation, standard error, FDR correction, fold change, log2FoldChange. The order effects the fold change values", "topics": [ "omu_summary" ] }, { "page": "PCA_plot", "title": "Create a PCA plot", "topics": [ "PCA_plot" ] }, { "page": "pie_chart", "title": "Create a pie chart", "topics": [ "pie_chart" ] }, { "page": "plate_omelette", "title": "plate_omelette Internal method for KEGG_Gather which parses flat text files", "topics": [ "plate_omelette", "plate_omelette.genes", "plate_omelette.KO", "plate_omelette.rxn" ] }, { "page": "plate_omelette_rxnko", "title": "Clean up orthology metadata", "topics": [ "plate_omelette_rxnko" ] }, { "page": "plot_bar", "title": "Create a bar plot", "topics": [ "plot_bar" ] }, { "page": "plot_boxplot", "title": "Create a box plot", "topics": [ "plot_boxplot" ] }, { "page": "plot_heatmap", "title": "Create a heatmap", "topics": [ "plot_heatmap" ] }, { "page": "plot_rf_PCA", "title": "plot_rf_PCA", "topics": [ "plot_rf_PCA" ] }, { "page": "plot_variable_importance", "title": "plot_variable_importance", "topics": [ "plot_variable_importance" ] }, { "page": "plot_volcano", "title": "Create a volcano plot", "topics": [ "plot_volcano" ] }, { "page": "ra_table", "title": "Creates a ratio table from the count_fold_changes function output.", "topics": [ "ra_table" ] }, { "page": "random_forest", "title": "random_forest Perform a classification or regression random forest model", "topics": [ "random_forest" ] }, { "page": "read_metabo", "title": "Import a metabolomics count data frame", "topics": [ "read_metabo" ] }, { "page": "transform_metabolites", "title": "transform_metabolites", "topics": [ "transform_metabolites" ] }, { "page": "transform_samples", "title": "transform_samples", "topics": [ "transform_samples" ] } ], "_rundeps": [ "abind", "askpass", "backports", "boot", "broom", "car", "carData", "caret", "class", "cli", "clock", "codetools", "colorspace", "corrplot", "cowplot", "cpp11", "curl", "data.table", "Deriv", "diagram", "digest", "doBy", "dplyr", "dunn.test", "e1071", "farver", "FlexParamCurve", "foreach", "forecast", "Formula", "fracdiff", "FSA", "future", "future.apply", "generics", "ggfortify", "ggplot2", "globals", "glue", "gower", "gridExtra", "gtable", "hardhat", "httr", "ipred", "isoband", "iterators", "jsonlite", "KernSmooth", "labeling", "lattice", "lava", "lifecycle", "listenv", "lme4", "lmtest", "lubridate", "magrittr", "MASS", "Matrix", "MatrixModels", "mgcv", "microbenchmark", "mime", "minqa", "ModelMetrics", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "parallelly", "pbkrtest", "pillar", "pkgconfig", "plotrix", "plyr", "pROC", "prodlim", "progressr", "proxy", "purrr", "quantreg", "R6", "randomForest", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "recipes", "reformulas", "reshape2", "rlang", "rpart", "rstatix", "S7", "scales", "shape", "SparseM", "sparsevctrs", "SQUAREM", "stringi", "stringr", "survival", "sys", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tzdb", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "Omu_vignette.Rmd", "filename": "Omu_vignette.html", "title": "omu, a Metabolomics Analysis R Package", "author": "Connor R. 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