{ "_id": "6a1acd5d1d7bb097a09df21f", "Package": "hermes", "Title": "Preprocessing, analyzing, and reporting of RNA-seq data", "Type": "Package", "Date": "2025-09-09", "Version": "1.17.0", "Authors@R": "c(\nperson(\"Daniel\", \"Sabanés Bové\", email = \"daniel.sabanes_bove@rconis.com\", role = c(\"aut\", \"cre\")),\nperson(\"Namrata\", \"Bhatia\", role = \"aut\"),\nperson(\"Stefanie\", \"Bienert\", role = \"aut\"),\nperson(\"Benoit\", \"Falquet\", role = \"aut\"),\nperson(\"Haocheng\", \"Li\", role = \"aut\"),\nperson(\"Jeff\", \"Luong\", role = \"aut\"),\nperson(\"Lyndsee\", \"Midori Zhang\", email = \"zhang.lyndsee@gene.com\", role = \"aut\"),\nperson(\"Alex\", \"Richardson\", role = \"aut\"),\nperson(\"Simona\", \"Rossomanno\", role = \"aut\"),\nperson(\"Tim\", \"Treis\", role = \"aut\"),\nperson(\"Mark\", \"Yan\", role = \"aut\"),\nperson(\"Naomi\", \"Chang\", role = \"aut\"),\nperson(\"Chendi\", \"Liao\", email = \"chendi.liao@roche.com\", role = \"aut\"),\nperson(\"Carolyn Zhang\", role = \"aut\"),\nperson(\"Joseph N.\", \"Paulson\", email = \"paulson.joseph@gene.com\", role = \"aut\"),\nperson(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\"))\n)", "Description": "Provides classes and functions for quality control,\nfiltering, normalization and differential expression analysis\nof pre-processed `RNA-seq` data. Data can be imported from\n`SummarizedExperiment` as well as `matrix` objects and can be\nannotated from `BioMart`. Filtering for genes without too low\nexpression or containing required annotations, as well as\nfiltering for samples with sufficient correlation to other\nsamples or total number of reads is supported. The standard\nnormalization methods including cpm, rpkm and tpm can be used,\nand 'DESeq2` as well as voom differential expression analyses\nare available.", "License": "Apache License 2.0", "URL": "https://insightsengineering.github.io/hermes/", "BugReports": "https://github.com/insightsengineering/hermes/issues", "VignetteBuilder": "knitr", "RdMacros": "Rdpack", "biocViews": "RNASeq, DifferentialExpression, Normalization,\nPreprocessing, QualityControl", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.0", "Collate": "'GeneSpec-class.R' 'HermesData-validate.R'\n'HermesData-class.R' 'HermesData-methods.R'\n'argument_convention.R' 'assertthat.R' 'calc_cor.R'\n'checkmate.R' 'connections.R' 'data.R' 'differential.R'\n'dplyr_compatibility.R' 'draw_barplot.R' 'draw_boxplot.R'\n'draw_heatmap.R' 'draw_scatterplot.R' 'graphs.R' 'join_cdisc.R'\n'normalization.R' 'package.R' 'pca.R' 'pca_cor_samplevar.R'\n'quality.R' 'top_genes.R' 'utils.R'", "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev perl\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:33 UTC", "RemoteUrl": "https://github.com/bioc/hermes", "RemoteRef": "HEAD", "RemoteSha": "f49637da43a95a7c41468a51cfb575db834228ed", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:05:10 UTC", "User": "root" }, "Author": "Daniel Sabanés Bové [aut, cre],\nNamrata Bhatia [aut],\nStefanie Bienert [aut],\nBenoit Falquet [aut],\nHaocheng Li [aut],\nJeff Luong [aut],\nLyndsee Midori Zhang [aut],\nAlex Richardson [aut],\nSimona Rossomanno [aut],\nTim Treis [aut],\nMark Yan [aut],\nNaomi Chang [aut],\nChendi Liao [aut],\nCarolyn Zhang [aut],\nJoseph N. Paulson [aut],\nF. Hoffmann-La Roche AG [cph, fnd]", "Maintainer": "Daniel Sabanés Bové ", "MD5sum": "8a58fafd0ced5519e48660ff3ad6b05b", "_user": "bioc", "_type": "src", "_file": "hermes_1.17.0.tar.gz", "_fileid": "75285d923ee0008e9f829ca84f7862c729999636ea134da96fd8f3bca91677f0", "_filesize": 4428480, "_sha256": "75285d923ee0008e9f829ca84f7862c729999636ea134da96fd8f3bca91677f0", "_created": "2026-05-30T08:05:10.000Z", "_published": "2026-05-30T11:43:24.954Z", "_jobs": [ { "job": 78635456469, "time": 201, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306717708" }, { "job": 78635456468, "time": 623, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7306758741" }, { "job": 78635456473, "time": 549, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7306751701" }, { "job": 78635456467, "time": 425, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7307925651" }, { "job": 78635456478, "time": 432, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7307925993" }, { "job": 78635166247, "time": 328, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306697462" }, { "job": 78635456461, "time": 160, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306713594" }, { "job": 78635456465, "time": 553, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7306752226" }, { "job": 78635456466, "time": 642, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7306760785" }, { "job": 78635456472, "time": 581, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7306754915" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/hermes", "_commit": { "id": "f49637da43a95a7c41468a51cfb575db834228ed", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381053 }, "_maintainer": { "name": "Daniel Sabanés Bové", "email": "daniel.sabanes_bove@rconis.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "ggfortify", "role": "Depends" }, { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "SummarizedExperiment", "version": ">= 1.16", "role": "Depends" }, { "package": "assertthat", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "biomaRt", "role": "Imports" }, { "package": "checkmate", "version": ">= 2.1", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "EnvStats", "role": "Imports" }, { "package": "forcats", "version": ">= 1.0.0", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "version": ">= 0.9", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "matrixStats", "version": ">= 1.5.0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "MultiAssayExperiment", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "R6", "role": "Imports" }, { "package": "Rdpack", "version": ">= 2.6.2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "DelayedArray", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "httr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "statmod", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.2.2", "role": "Suggests" }, { "package": "vdiffr", "version": ">= 1.0.8", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-37", "n": 3 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23" } ], "_topics": [ "rnaseq", "differentialexpression", "normalization", "preprocessing", "qualitycontrol", "rna-seq", "statistical-engineering" ], "_stars": 12, "_contributors": [ { "user": "luongj3", "count": 63, "uuid": 87994544 }, { "user": "danielinteractive", "count": 60, "uuid": 1071227 }, { "user": "bienerts", "count": 57, "uuid": 75780729 }, { "user": "namratabhatia", "count": 44, "uuid": 53239049 }, { "user": "colinisstudent", "count": 36, "uuid": 87772156 }, { "user": "walkowif", "count": 20, "uuid": 59475134 }, { "user": "insights-engineering-bot", "count": 18, "uuid": 68416928 }, { "user": "cicdguy", "count": 14, "uuid": 26552821 }, { "user": "codesformochi", "count": 11, "uuid": 39424598 }, { "user": "arkadiuszbeer", "count": 11, "uuid": 86738093 }, { "user": "knightdave", "count": 10, "uuid": 13086223 }, { "user": "bfalquet", "count": 8, "uuid": 64274616 }, { "user": "pawelru", "count": 7, "uuid": 12943682 }, { "user": "vedhav", "count": 6, "uuid": 49812166 }, { "user": "m7pr", "count": 6, "uuid": 133694481 }, { "user": "kpagacz", "count": 4, "uuid": 24480246 }, { "user": "timtreis", "count": 3, "uuid": 12818242 }, { "user": "denisovan31415", "count": 3, "uuid": 12874196 }, { "user": "fanooel", "count": 2, "uuid": 1877788 }, { "user": "alexjoerich", "count": 2, "uuid": 73207272 }, { "user": "mhallal1", "count": 2, "uuid": 86970066 }, { "user": "waddella", "count": 1, "uuid": 7786462 }, { "user": "gravesti", "count": 1, "uuid": 83659704 }, { "user": "polkas", "count": 1, "uuid": 10676545 }, { "user": "moronip81", "count": 1, "uuid": 130590957 }, { "user": "nikolas-burkoff", "count": 1, "uuid": 15201933 }, { "user": "tomszosz", "count": 1, "uuid": 42359321 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 456, "source": "https://www.bioconductor.org/packages/stats/bioc/hermes" }, "_devurl": "https://github.com/insightsengineering/hermes", "_pkgdown": "https://insightsengineering.github.io/hermes/", "_searchresults": 45, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hermes.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/insightsengineering/hermes", "_realowner": "bioc", "_cranurl": false, "_exports": [ ".ConnectionBiomart", ".row_data_annotation_cols", "%>%", "add_quality_flags", "annotation", "annotation<-", "assert_proportion", "autoplot", "calc_pca", "cat_with_newline", "check_proportion", "col_data_with_genes", "colMeanZscores", "colPrinComp1", "connect_biomart", "control_normalize", "control_quality", "correlate", "counts", "counts<-", "cut_quantile", "df_cols_to_factor", "diff_expression", "draw_barplot", "draw_boxplot", "draw_genes_barplot", "draw_heatmap", "draw_libsize_densities", "draw_libsize_hist", "draw_libsize_qq", "draw_nonzero_boxplot", "draw_scatterplot", "expect_proportion", "extraColDataNames", "extraRowDataNames", "filter", "gene_spec", "genes", "GeneSpec", "get_low_depth", "get_low_expression", "get_tech_failure", "h_all_duplicated", "h_cpm", "h_df_factors_with_explicit_na", "h_diff_expr_deseq2", "h_diff_expr_voom", "h_draw_boxplot_df", "h_ensembl_to_entrez_ids", "h_get_annotation_biomart", "h_get_granges_by_id", "h_get_size_biomart", "h_has_req_annotations", "h_low_depth_flag", "h_low_expression_flag", "h_map_pos", "h_parens", "h_pca_df_r2_matrix", "h_pca_var_rsquared", "h_rlog", "h_rpkm", "h_short_list", "h_strip_prefix", "h_tech_failure_flag", "h_tpm", "h_unique_labels", "h_voom", "h_vst", "HermesData", "HermesDataFromMatrix", "inner_join_cdisc", "is_class", "is_constant", "is_counts_vector", "is_hermes_data", "is_list_with", "isEmpty", "lapply", "metadata", "metadata<-", "normalize", "one_provided", "prefix", "query", "rename", "samples", "set_tech_failure", "show", "summary", "test_proportion", "top_genes", "wrap_in_mae" ], "_datasets": [ { "name": "expression_set", "title": "Example 'ExpressionSet' Data", "object": "expression_set", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false }, { "name": "hermes_data", "title": "Example 'HermesData' Data", "object": "hermes_data", "class": [ "HermesData" ], "fields": [], "table": false, "tojson": false }, { "name": "multi_assay_experiment", "title": "Example 'MultiAssayExperiment' Data", "object": "multi_assay_experiment", "class": [ "MultiAssayExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "summarized_experiment", "title": "Example 'SummarizedExperiment' Data", "object": "summarized_experiment", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "hermes-package", "title": "'hermes' Package", "topics": [ "hermes-package", "hermes" ] }, { "page": "quality_flags", "title": "Add Quality Flags", "topics": [ "add_quality_flags", "get_low_depth", "get_low_expression", "get_tech_failure", "h_low_depth_flag", "h_low_expression_flag", "h_tech_failure_flag" ] }, { "page": "all_na", "title": "Checks Whether All Missing", "topics": [ "all_na" ] }, { "page": "annotation", "title": "Annotation Accessor and Setter", "topics": [ ".row_data_annotation_cols", "annotation", "annotation,AnyHermesData-method", "annotation<-,AnyHermesData,DataFrame-method" ] }, { "page": "assertion_arguments", "title": "Standard Assertion Arguments", "topics": [ "assertion_arguments" ] }, { "page": "assertions", "title": "Additional Assertions for 'assert_that'", "topics": [ "assertions", "is_class", "is_constant", "is_counts_vector", "is_hermes_data", "is_list_with", "one_provided" ] }, { "page": "plot_all", "title": "All Standard Plots in Default Setting", "topics": [ "autoplot,AnyHermesData-method", "plot_all" ] }, { "page": "calc_pca", "title": "Principal Components Analysis Calculation", "topics": [ ".HermesDataPca", "calc_pca", "HermesDataPca", "HermesDataPca-class" ] }, { "page": "cat_with_newline", "title": "Concatenate and Print with Newline", "topics": [ "cat_with_newline" ] }, { "page": "cbind", "title": "Column Binding of 'AnyHermesData' Objects", "topics": [ "cbind" ] }, { "page": "check_proportion", "title": "Check for proportion", "topics": [ "assert_proportion", "check_proportion", "expect_proportion", "test_proportion" ] }, { "page": "col_data_with_genes", "title": "Sample Variables with Selected Gene Information", "topics": [ "col_data_with_genes" ] }, { "page": "colMeanZscores", "title": "Mean Z-score Gene Signature", "topics": [ "colMeanZscores" ] }, { "page": "colPrinComp1", "title": "First Principal Component (PC1) Gene Signature", "topics": [ "colPrinComp1" ] }, { "page": "connect_biomart", "title": "Connection to 'BioMart'", "topics": [ ".ConnectionBiomart", "ConnectionBiomart", "ConnectionBiomart-class", "connect_biomart" ] }, { "page": "control_normalize", "title": "Control Settings for Counts Normalization", "topics": [ "control_normalize" ] }, { "page": "control_quality", "title": "Control for Specified Quality Flags", "topics": [ "control_quality" ] }, { "page": "correlate", "title": "Generic Function for Correlation Calculations", "topics": [ "correlate" ] }, { "page": "calc_cor", "title": "Correlation between Sample Counts of 'AnyHermesData'", "topics": [ ".HermesDataCor", "autoplot,HermesDataCor-method", "calc_cor", "correlate,AnyHermesData-method", "HermesDataCor", "HermesDataCor-class" ] }, { "page": "pca_cor_samplevar", "title": "Correlation of Principal Components with Sample Variables", "topics": [ ".HermesDataPcaCor", "autoplot,HermesDataPcaCor-method", "correlate,HermesDataPca-method", "HermesDataPcaCor", "HermesDataPcaCor-class", "pca_cor_samplevar" ] }, { "page": "counts", "title": "Counts Accessor and Setter", "topics": [ "counts", "counts,AnyHermesData-method", "counts<-,AnyHermesData,matrix-method" ] }, { "page": "cut_quantile", "title": "Cutting a Numeric Vector into a Factor of Quantile Bins", "topics": [ "cut_quantile" ] }, { "page": "df_cols_to_factor", "title": "Conversion of Eligible Columns to Factor Variables in a 'DataFrame'", "topics": [ "df_cols_to_factor" ] }, { "page": "diff_expression", "title": "Differential Expression Analysis", "topics": [ ".HermesDataDiffExpr", "autoplot,HermesDataDiffExpr-method", "diff_expression", "HermesDataDiffExpr", "HermesDataDiffExpr-class" ] }, { "page": "draw_barplot", "title": "Barplot for Gene Expression Percentiles", "topics": [ "draw_barplot" ] }, { "page": "draw_boxplot", "title": "Boxplot for Gene Expression Values", "topics": [ "draw_boxplot", "h_draw_boxplot_df" ] }, { "page": "draw_genes_barplot", "title": "Stacked Barplot of Low Expression Genes by Chromosome", "topics": [ "draw_genes_barplot" ] }, { "page": "draw_heatmap", "title": "Heatmap for Gene Expression Counts", "topics": [ "draw_heatmap" ] }, { "page": "draw_libsize_densities", "title": "Density Plot of (Log) Counts Distributions", "topics": [ "draw_libsize_densities" ] }, { "page": "draw_libsize_hist", "title": "Histogram of Library Sizes", "topics": [ "draw_libsize_hist" ] }, { "page": "draw_libsize_qq", "title": "Q-Q Plot of Library Sizes", "topics": [ "draw_libsize_qq" ] }, { "page": "draw_nonzero_boxplot", "title": "Boxplot of Non-Zero Genes", "topics": [ "draw_nonzero_boxplot" ] }, { "page": "draw_scatterplot", "title": "Scatterplot for Gene Expression Values", "topics": [ "draw_scatterplot" ] }, { "page": "expression_set", "title": "Example 'ExpressionSet' Data", "topics": [ "expression_set" ] }, { "page": "extra_data_names", "title": "Extra Variable Names Accessor Methods", "topics": [ "extraColDataNames", "extraColDataNames,AnyHermesData-method", "extraRowDataNames", "extraRowDataNames,AnyHermesData-method", "extra_data_names" ] }, { "page": "filter", "title": "Filter 'AnyHermesData' on Subset Passing Default QC Flags", "topics": [ "filter", "filter,AnyHermesData-method", "filter,data.frame-method", "filter,ts-method" ] }, { "page": "gene_spec", "title": "'GeneSpec' Constructor", "topics": [ "gene_spec" ] }, { "page": "genes", "title": "Gene IDs Accessor", "topics": [ "genes", "genes,AnyHermesData-method" ] }, { "page": "GeneSpec", "title": "R6 Class Representing a Gene (Signature) Specification", "topics": [ "GeneSpec" ] }, { "page": "h_all_duplicated", "title": "Finding All Duplicates in Vector", "topics": [ "h_all_duplicated" ] }, { "page": "h_df_factors_with_explicit_na", "title": "Conversion to Factors with Explicit Missing Level in a 'data.frame'", "topics": [ "h_df_factors_with_explicit_na" ] }, { "page": "h_diff_expr_deseq2", "title": "'DESeq2' Differential Expression Analysis", "topics": [ "h_diff_expr_deseq2" ] }, { "page": "h_diff_expr_voom", "title": "'limma'/voom Differential Expression Analysis", "topics": [ "h_diff_expr_voom" ] }, { "page": "h_ensembl_to_entrez_ids", "title": "Translation of 'Ensembl' to 'Entrez' Gene IDs", "topics": [ "h_ensembl_to_entrez_ids" ] }, { "page": "h_get_annotation_biomart", "title": "Get Annotations from 'BioMart'", "topics": [ "h_get_annotation_biomart" ] }, { "page": "h_get_granges_by_id", "title": "Conversion of 'BioMart' Coordinates into 'GRanges'", "topics": [ "h_get_granges_by_id" ] }, { "page": "h_get_size_biomart", "title": "Total Length of All Exons for Genes", "topics": [ "h_get_size_biomart" ] }, { "page": "h_has_req_annotations", "title": "Predicate for Required Annotations", "topics": [ "h_has_req_annotations" ] }, { "page": "h_map_pos", "title": "Helper Function For Matching Map Values to Names", "topics": [ "h_map_pos" ] }, { "page": "h_parens", "title": "Parenthesize a Character Vector", "topics": [ "h_parens" ] }, { "page": "h_pca_df_r2_matrix", "title": "Calculation of R2 Matrix between Sample Variables and Principal Components", "topics": [ "h_pca_df_r2_matrix" ] }, { "page": "h_pca_var_rsquared", "title": "Calculation of R2 between Sample Variable and Principal Components", "topics": [ "h_pca_var_rsquared" ] }, { "page": "h_short_list", "title": "Make a Short List of a Character Vector", "topics": [ "h_short_list" ] }, { "page": "h_strip_prefix", "title": "Stripping Prefix from Gene IDs", "topics": [ "h_strip_prefix" ] }, { "page": "h_unique_labels", "title": "Creation of Unique Labels", "topics": [ "h_unique_labels" ] }, { "page": "hermes_data", "title": "Example 'HermesData' Data", "topics": [ "hermes_data" ] }, { "page": "HermesData-class", "title": "'HermesData' and 'RangedHermesData'", "topics": [ ".HermesData", ".RangedHermesData", "AnyHermesData", "AnyHermesData-class", "HermesData", "HermesData-class", "HermesDataFromMatrix", "RangedHermesData", "RangedHermesData-class" ] }, { "page": "inner_join_cdisc", "title": "Inner Joining a Genes with a CDISC Data Set", "topics": [ "inner_join_cdisc" ] }, { "page": "isEmpty", "title": "Checking for Empty 'SummarizedExperiment'", "topics": [ "isEmpty", "isEmpty,SummarizedExperiment-method" ] }, { "page": "lapply", "title": "'lapply' method for 'MultiAssayExperiment'", "topics": [ "lapply", "lapply,MultiAssayExperiment-method" ] }, { "page": "metadata", "title": "Metadata Accessor and Setter", "topics": [ "metadata" ] }, { "page": "multi_assay_experiment", "title": "Example 'MultiAssayExperiment' Data", "topics": [ "multi_assay_experiment" ] }, { "page": "normalize", "title": "Normalization of 'AnyHermesData' Objects", "topics": [ "h_cpm", "h_rlog", "h_rpkm", "h_tpm", "h_voom", "h_vst", "normalize", "normalize,AnyHermesData-method" ] }, { "page": "prefix", "title": "Prefix Accessor", "topics": [ "prefix" ] }, { "page": "query", "title": "Query Gene Annotations from a Connection", "topics": [ "query", "query,character,ConnectionBiomart-method" ] }, { "page": "rbind", "title": "Row Binding of 'AnyHermesData' Objects", "topics": [ "rbind" ] }, { "page": "rename", "title": "Renaming Contents of 'SummarizedExperiment' Objects", "topics": [ "rename", "rename,data.frame-method", "rename,SummarizedExperiment-method" ] }, { "page": "samples", "title": "Sample IDs Accessor", "topics": [ "samples", "samples,AnyHermesData-method" ] }, { "page": "set_tech_failure", "title": "Set Technical Failure Flags", "topics": [ "set_tech_failure" ] }, { "page": "show", "title": "Show Method for 'AnyHermesData' Objects", "topics": [ "show", "show,HermesData-method", "show,RangedHermesData-method" ] }, { "page": "subset", "title": "Subsetting 'AnyHermesData' Objects", "topics": [ "subset" ] }, { "page": "summarized_experiment", "title": "Example 'SummarizedExperiment' Data", "topics": [ "summarized_experiment" ] }, { "page": "summary", "title": "Summary Method for 'AnyHermesData' Objects", "topics": [ ".HermesDataSummary", "HermesDataSummary", "HermesDataSummary-class", "show,HermesDataSummary-method", "summary", "summary,AnyHermesData-method" ] }, { "page": "top_genes", "title": "Derivation of Top Genes", "topics": [ ".HermesDataTopGenes", "autoplot,HermesDataTopGenes-method", "HermesDataTopGenes", "HermesDataTopGenes-class", "top_genes" ] }, { "page": "validate", "title": "Internal Helper Functions for Validation of 'AnyHermesData' Objects", "topics": [ "validate", "validate_cols", "validate_col_data", "validate_counts", "validate_names", "validate_prefix", "validate_row_data" ] }, { "page": "wrap_in_mae", "title": "Wrap in MAE", "topics": [ "wrap_in_mae" ] } ], "_pkglogo": "https://github.com/bioc/hermes/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/hermes/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "assertthat", "backports", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "blob", "cachem", "checkmate", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "DESeq2", "digest", "doParallel", "dplyr", "edgeR", "EnvStats", "farver", "fastmap", "filelock", "forcats", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "GetoptLong", "ggfortify", "ggplot2", "ggrepel", "GlobalOptions", "glue", "gridExtra", "gtable", "hms", "httr", "httr2", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "MultiAssayExperiment", "nortest", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "Rdpack", "rjson", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "xml2", "XVector" ], "_vignettes": [ { "source": "hermes.Rmd", "filename": "hermes.html", "title": "Introduction to hermes", "author": "Daniel Sabanés Bové, Namrata Bhatia, Stefanie Bienert, Benoit Falquet, Haocheng Li, Jeff Luong, Lyndsee Midori Zhang, Alex Richardson, Simona Rossomanno, Tim Treis, Mark Yan, Naomi Chang, Chendi Liao, Carolyn Zhang, Joseph N. Paulson, Daniel Sabanés Bové", "engine": "knitr::rmarkdown", "headings": [ "Acknowledgments", "Installation", "BioConductor", "GitHub", "Introduction", "Importing Data", "Importing a SummarizedExperiment", "Importing an ExpressionSet", "Importing a Matrix", "Annotations", "Connection to Database", "Querying and Saving Annotations", "Quality Control Flags", "Automatic Gene and Sample Flagging", "Manual Sample Flagging", "Accessing Flags", "Filtering Data", "Based on Default QC Flags", "Based on Custom Variables", "Normalizing Counts", "Descriptive Plots", "Simple Plots", "Top Genes", "Heatmap of Genes among Samples", "Correlation between Samples", "Principal Components", "PCA of Samples", "Correlation with Sample Variables", "QC Report Template", "Differential Expression", "Summary", "Session Info" ], "created": "2024-01-18 17:55:10", "modified": "2025-09-09 03:41:55", "commits": 3 } ], "_score": 7.800579621569131, "_indexed": true, "_nocasepkg": "hermes", "_universes": [ "bioc", "insightsengineering" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T08:09:30.000Z", "distro": "noble", "commit": "f49637da43a95a7c41468a51cfb575db834228ed", "fileid": "2bb421fc878dc834b9e2dd8220ea4bb99cd23045a285c0cff933be337f35ac6b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010" }, { "r": "4.6.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T08:09:46.000Z", "distro": "noble", "commit": "f49637da43a95a7c41468a51cfb575db834228ed", "fileid": "d68748e259b39e1f3b712e36afc162401b9961aaac9b87d40c577cf92eb6a3e3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010" }, { "r": "4.5.3", "os": "mac", "version": "1.17.0", "date": "2026-05-30T11:37:20.000Z", "commit": "f49637da43a95a7c41468a51cfb575db834228ed", "fileid": "921abcd0886e38e4b248592866bbd3281511e2c5a93c23634d071269bfcd9849", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010" }, { "r": "4.6.0", "os": "mac", "version": "1.17.0", "date": "2026-05-30T11:37:21.000Z", "commit": "f49637da43a95a7c41468a51cfb575db834228ed", "fileid": "db02e0a6ada1dcb8e9944f7a5018447f63e9189c2c1a7f1c19dd409d205b0d93", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.0", "date": "2026-05-30T08:08:44.000Z", "commit": "f49637da43a95a7c41468a51cfb575db834228ed", "fileid": "b1db8241e331ef92ed2d2dd5819df7621d2b5652d65be97aa780d51cf66c7dce", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010" }, { "r": "4.7.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:07:34.000Z", "commit": "f49637da43a95a7c41468a51cfb575db834228ed", "fileid": "4a067e4b1a8068c62e6b42b4e9a1e8ec9f971b7673a2ee8806db136eb8c16856", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010" }, { "r": "4.5.3", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:08:28.000Z", "commit": "f49637da43a95a7c41468a51cfb575db834228ed", "fileid": "3051567d1b9bcd88ec088408e0b3f2e5f6e9984dd9df4e1824376b4f92a5539e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010" }, { "r": "4.6.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:07:54.000Z", "commit": "f49637da43a95a7c41468a51cfb575db834228ed", "fileid": "575f1781e87cd55d03eb6fc9a96ec034673310135ce03239891deb3485a22cbc", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678697010" } ] }