{ "_id": "6ac28e02d743750d376d8c60", "Package": "ExpHunterSuite", "Title": "Package for the Comprehensive Analysis of Transcriptomic Data", "Version": "1.20.0", "Author": "James Perkins", "Maintainer": "James Perkins ", "Authors@R": "c(\nperson(\"James\", \"Perkins\", email = \"jimrperkins@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4108-096X\")),\nperson(\"Pedro\", \"Seoane Zonjic\", email = \"seoanezonjic@uma.es\", role = \"aut\", comment = c(ORCID = \"0000-0002-3020-1415\")),\nperson(\"Fernando\", \"Moreno Jabato\", email = \"fmjabato@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-7498-1962\")),\nperson(\"José\", \"Córdoba Caballero\", email = \"josecordoba1995@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-1821-5742\")),\nperson(\"Elena\", \"Rojano Rivera\", email = \"elenarojano@outlook.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-2678-710X\")),\nperson(\"Rocio\", \"Bautista Moreno\", email = \"rociobm@uma.es\", role = \"aut\", comment = c(ORCID = \"0000-0003-1685-8119\")),\nperson(\"M. Gonzalo\", \"Claros\", email = \"claros@uma.es\", role = \"aut\", comment = c(ORCID = \"0000-0002-0112-3550\")),\nperson(\"Isabel\", \"Gonzalez Gayte\", email = \"isabel.ggayte@gmail.com\", role = \"aut\"),\nperson(\"Juan Antonio\", \"García Ranea\", email = \"ranea@uma.es\", role = \"aut\", comment = c(ORCID = \"0000-0003-0327-1837\"))\n)", "Description": "The ExpHunterSuite implements a comprehensive protocol for\nthe analysis of transcriptional data using established R\npackages and combines their results. It covers key steps\nincluding differential expression analysis, co-expression\nanalysis, and functional enrichment for RNA-seq data. The\npackage provides interactive R functions as well as\ncommand-line scripts that wrap these functions.", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "biocViews": "GeneExpressionWorkflow", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev libgmp3-dev make libmagick++-dev\ngsfonts libbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev pari-gp libx11-dev xz-utils zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:44:49 UTC", "RemoteUrl": "https://github.com/bioc/ExpHunterSuite", "RemoteRef": "RELEASE_3_23", "RemoteSha": "1960a2c9f7f2ae5f261065c1eb3b4229e4e7649c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-04 17:18:59 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "ExpHunterSuite_1.20.0.tar.gz", 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"install_DEgenes_hunter", "load_and_parse_gmt", "load_synth_dataset", "main_clusters_to_enrichment", "main_degenes_Hunter", "main_functional_hunter", "multienricher_gsea", "multienricher_ora", "multienricher_topGO", "parse_pseudocounts", "ppv", "recall", "rtable2measures", "spc", "target_generation", "write_clusters_to_enrichment", "write_df_list_as_tables", "write_enrich_files", "write_expression_report", "write_functional_report" ], "_datasets": [ { "name": "degh_output", "title": "Output data from the main_degenes_Hunter function", "object": "degh_output", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "target", "title": "Target data containing sample information for the toc data", "object": "target", "class": [ "data.frame" ], "fields": [ "sample", "treat" ], "rows": 7, "table": true, "tojson": true }, { "name": "toc", "title": "Table of counts dummy dataset for DEgeneHunter examples", "object": "toc", "class": [ "data.frame" ], "fields": [ "CTL_1", "CTL_2", "CTL_3", "CTL_4", "epm2a_1", "epm2a_2", "epm2a_3" ], "rows": 530, "table": true, "tojson": true } ], "_help": [ { "page": "acc", "title": "Calculates accuracy from a measures dataframe", "topics": [ "acc" ] }, { "page": "degh_output", "title": "Output data from the main_degenes_Hunter function", "topics": [ "degh_output" ] }, { "page": "degsynth", "title": "Main function to generate synthetic data using an specific exponential distribution for logFC", "topics": [ "degsynth" ] }, { "page": "download_latest_kegg_db", "title": "download kegg db for a given organism", "topics": [ "download_latest_kegg_db" ] }, { "page": "extract_from_cm", "title": "Extract value from confusion matrix", "topics": [ "extract_from_cm" ] }, { "page": "fcfunc", "title": "Custom function to generate exponentially degradated foldchange range", "topics": [ "fcfunc" ] }, { "page": "fmeasure", "title": "Calculates F measure from a measures dataframe", "topics": [ "fmeasure" ] }, { "page": "get_kegg_db_path", "title": "get path for KEGG db for downloading/usage", "topics": [ "get_kegg_db_path" ] }, { "page": "get_org_db", "title": "Obtain an org_db object from a current_organism_info, obtained from subsetting the results of get_organism_table()", "topics": [ "get_org_db" ] }, { "page": "get_organism_table", "title": "Table with information abaut all organism available", "topics": [ "get_organism_table" ] }, { "page": "get_stats", "title": "Function to calculate full set of measures from a confusion data frame", "topics": [ "get_stats" ] }, { "page": "get_stats_from_cm", "title": "Obtain full set of measures from a confusion matrix", "topics": [ "get_stats_from_cm" ] }, { "page": "get_unexported_function", "title": "Method used to import hidden functions legally for CRAN check", "topics": [ "get_unexported_function" ] }, { "page": "ht2logFCPlot", "title": "Function to generate scatter plot for each gene in a hunter table and show logFC per package taking into account the variablity between them", "topics": [ "ht2logFCPlot" ] }, { "page": "install_DEgenes_hunter", "title": "Hunter installation Function", "topics": [ "install_DEgenes_hunter" ] }, { "page": "load_and_parse_gmt", "title": "Load a GMT format file and return a dataframe in correct format", "topics": [ "load_and_parse_gmt" ] }, { "page": "load_synth_dataset", "title": "Loads Hunter DEG analysis table and simulated TRUE DEG vector. Concat in training/testing ML data frame format and returns it.", "topics": [ "load_synth_dataset" ] }, { "page": "load_WGCNA_results", "title": "Loads stored WGCNA results in DEgenes Hunter expression analysis package folder and returns in compact object", "topics": [ "load_WGCNA_results" ] }, { "page": "main_clusters_to_enrichment", "title": "Perform enrichment analysis on multiple lists of genes", "topics": [ "main_clusters_to_enrichment" ] }, { "page": "main_degenes_Hunter", "title": "Main DEgenes Hunter Function", "topics": [ "main_degenes_Hunter" ] }, { "page": "main_functional_hunter", "title": "Perform Functional analysis with different enrichment corpora.", "topics": [ "main_functional_hunter" ] }, { "page": "multienricher_gsea", "title": "Perform gsea enrichment analysis of a list of genes", "topics": [ "multienricher_gsea" ] }, { "page": "multienricher_ora", "title": "Perform ORA enrichment analysis of a list of genes", "topics": [ "multienricher_ora" ] }, { "page": "multienricher_topGO", "title": "Perform topGO enrichment analysis of a list of genes", "topics": [ "multienricher_topGO" ] }, { "page": "parallel_list", "title": "Parallelize function execution in list with multiple elements", "topics": [ "parallel_list" ] }, { "page": "parse_pseudocounts", "title": "main_parse_pseudocounts Functions that loads pseudommappers results and complite it into a table of counts", "topics": [ "parse_pseudocounts" ] }, { "page": "ppv", "title": "Calculates Positive Predictive Value from a measures dataframe", "topics": [ "ppv" ] }, { "page": "recall", "title": "Calculates Recall from a measures dataframe", "topics": [ "recall" ] }, { "page": "rtable2measures", "title": "Calculates emasures from result tables", "topics": [ "rtable2measures" ] }, { "page": "scale_data_matrix", "title": "Scale a matrix using minimum-maximum method", "topics": [ "scale_data_matrix" ] }, { "page": "scale_range", "title": "Funtion used to scale a vector of numeric values from (x_min,x_max) range to (y_min,y_max) range. f : R -> R (x_min, x_max) -> (y_min, y_max) vect - x_min f(vect,y_min,y_max) = ----- x (y_max - y_min) + y_min x_max - x_min", "topics": [ "scale_range" ] }, { "page": "spc", "title": "Calculates specificity from a measures dataframe", "topics": [ "spc" ] }, { "page": "STC", "title": "Function to Simulate Treatment-Control paired experiments for genes expression count tables. Pipeline inspired on TCC simulateReadCounts function", "topics": [ "STC" ] }, { "page": "target", "title": "Target data containing sample information for the toc data", "topics": [ "target" ] }, { "page": "target_generation", "title": "Function to generate targets file Load target file if it exists, otherwise use the -C and -T flags. Note target takes precedence over target.", "topics": [ "target_generation" ] }, { "page": "toc", "title": "Table of counts dummy dataset for DEgeneHunter examples", "topics": [ "toc" ] }, { "page": "translate_from_table", "title": "Translates a given gene ID using a dictionary. Note: one unknown ID can corresponds to many known ids.", "topics": [ "translate_from_table" ] }, { "page": "trycatch_pairwise_termsim", "title": "if pairwise_termsim throws an error, remove dup cat descriptions Only seems to be a problem with Reactome - to study further Further investigation re: number of cats also required", "topics": [ "trycatch_pairwise_termsim" ] }, { "page": "write_clusters_to_enrichment", "title": "Write Main clusters to enrichment output This function allows you to report the Functional analysis.", "topics": [ "write_clusters_to_enrichment" ] }, { "page": "write_df_list_as_tables", "title": "Function to write expression package results. Write to disk the results of each diff expression package", "topics": [ "write_df_list_as_tables" ] }, { "page": "write_enrich_files", "title": "Write enrichment files related to functional_hunter results list", "topics": [ "write_enrich_files" ] }, { "page": "write_expression_report", "title": "Write Main DEgenes Hunter report", "topics": [ "write_expression_report" ] }, { "page": "write_functional_report", "title": "Write Main DEgenes Hunter functional report This function allows you to report the Functional analysis.", "topics": [ "write_functional_report" ] } ], "_readme": "https://github.com/bioc/ExpHunterSuite/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "aisdk", "AnnotationDbi", "AnnotationHub", "annotatr", "ape", "aplot", "arrangements", "askpass", "assertthat", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "BiocVersion", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "boot", "broom", "BSgenome", "bslib", "ca", "cachem", "callr", "car", "carData", "caTools", "checkmate", "cigarillo", "cli", "clipr", "cluster", "clusterProfiler", "codetools", "colorspace", "contfrac", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "dendextend", "Deriv", "DESeq2", "deSolve", "diffcoexp", "DiffCorr", "digest", "dir.expiry", "doBy", "doParallel", "DOSE", "dplyr", "DT", "dynamicTreeCut", "edgeR", "egg", "ellipse", "elliptic", "emmeans", "enrichit", "enrichplot", "estimability", "evaluate", "exactRankTests", "FactoInvestigate", "FactoMineR", "farver", "fastcluster", "fastmap", "fdrtool", "filelock", "flashClust", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "forcats", "foreach", "forecast", "foreign", "formatR", "Formula", "fracdiff", "fs", "futile.logger", "futile.options", "gclus", "gdtools", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggforce", "ggfun", "ggiraph", "ggnewscale", "ggplot2", "ggplotify", "ggraph", "ggrepel", "ggridges", "ggtangle", "ggtree", "glmnet", "glue", "gmp", "GO.db", "GOSemSim", "GPArotation", "gplots", "graph", "graphite", "graphlayouts", "gridExtra", "gridGraphics", "gson", "gtable", "gtools", "haven", "heatmaply", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "httr2", "hypergeo", "igraph", "impute", "IRanges", "irlba", "isoband", "iterators", "jomo", "jquerylib", "jsonlite", "KEGGREST", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "leaps", "lifecycle", "limma", "lme4", "lmtest", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "mice", "miceadds", "mime", "minqa", "miRBaseVersions.db", "mitml", "mitools", "MKdescr", "MKinfer", "mnormt", "modelr", "multcompView", "multtest", "mvtnorm", "nlme", "nloptr", "nnet", "NOISeq", "numDeriv", "openssl", "ordinal", "otel", "pan", "patchwork", "pbkrtest", "pcaMethods", "permute", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "preprocessCore", "prettyunits", "processx", "progress", "promises", "ps", "psych", "purrr", "qap", "quantreg", "qvalue", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "Rdpack", "reactome.db", "ReactomePA", "readr", "reformulas", "regioneR", "registry", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "ROCR", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scatterpie", "scatterplot3d", "Seqinfo", "seriation", "shape", "showtext", "showtextdb", "snow", "SparseArray", "SparseM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "sysfonts", "systemfonts", "tibble", "tidydr", "tidygraph", "tidyr", "tidyselect", "tidytree", "timeDate", "tinytex", "topGO", "treeio", "TSP", "tweenr", "txdbmaker", "tximport", "tzdb", "ucminf", "UCSC.utils", "urca", "utf8", "vctrs", "vegan", "viridis", "viridisLite", "vroom", "webshot", "WGCNA", "withr", "xfun", "XML", "xml2", "XVector", "yaml", "yulab.utils", "zoo" ], "_vignettes": [ { "source": "hunter.Rmd", "filename": "hunter.html", "title": "The Expression Hunter Suite", "author": "James R. 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