Package: hermes 1.7.2.9003
Daniel Sabanés Bové
hermes: Preprocessing, analyzing, and reporting of RNA-seq data
Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.
Authors:
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hermes.pdf |hermes.html✨
hermes/json (API)
NEWS
| # Install 'hermes' in R: |
| install.packages('hermes', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/insightsengineering/hermes/issues
- expression_set - Example 'ExpressionSet' Data
- hermes_data - Example 'HermesData' Data
- multi_assay_experiment - Example 'MultiAssayExperiment' Data
- summarized_experiment - Example 'SummarizedExperiment' Data
On BioConductor:hermes-1.11.0(bioc 3.21)hermes-1.10.0(bioc 3.20)
rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering
Last updated 2 months agofrom:e7eb4b4ef6. Checks:OK: 6 WARNING: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 15 2024 |
| R-4.5-win | OK | Nov 15 2024 |
| R-4.5-linux | WARNING | Nov 15 2024 |
| R-4.4-win | OK | Nov 15 2024 |
| R-4.4-mac | OK | Nov 15 2024 |
| R-4.3-win | OK | Nov 15 2024 |
| R-4.3-mac | OK | Nov 15 2024 |
Exports:.ConnectionBiomart.row_data_annotation_cols%>%add_quality_flagsannotationannotation<-assert_proportionautoplotcalc_pcacat_with_newlinecheck_proportioncol_data_with_genescolMeanZscorescolPrinComp1connect_biomartcontrol_normalizecontrol_qualitycorrelatecountscounts<-cut_quantiledf_cols_to_factordiff_expressiondraw_barplotdraw_boxplotdraw_genes_barplotdraw_heatmapdraw_libsize_densitiesdraw_libsize_histdraw_libsize_qqdraw_nonzero_boxplotdraw_scatterplotexpect_proportionextraColDataNamesextraRowDataNamesfiltergene_specgenesGeneSpecget_low_depthget_low_expressionget_tech_failureh_all_duplicatedh_cpmh_df_factors_with_explicit_nah_diff_expr_deseq2h_diff_expr_voomh_draw_boxplot_dfh_ensembl_to_entrez_idsh_get_annotation_biomarth_get_granges_by_idh_get_size_biomarth_has_req_annotationsh_low_depth_flagh_low_expression_flagh_map_posh_parensh_pca_df_r2_matrixh_pca_var_rsquaredh_rlogh_rpkmh_short_listh_strip_prefixh_tech_failure_flagh_tpmh_unique_labelsh_voomh_vstHermesDataHermesDataFromMatrixinner_join_cdiscis_classis_constantis_counts_vectoris_hermes_datais_list_withisEmptylapplymetadatametadata<-normalizeone_providedprefixqueryrenamesamplesset_tech_failureshowsummarytest_proportiontop_geneswrap_in_mae
Dependencies:abindAnnotationDbiaskpassassertthatbackportsBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64blobcachemcheckmatecirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdbplyrDelayedArrayDESeq2digestdoParalleldplyredgeREnvStatsfansifarverfastmapfilelockforcatsforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggfortifyggplot2ggrepelGlobalOptionsgluegridExtragtablehmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentmunsellnlmenortestopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRdpackrjsonrlangRSQLiteS4ArraysS4VectorsscalesshapesnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrxml2XVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'hermes' Package | hermes-package hermes |
| Add Quality Flags | add_quality_flags get_low_depth get_low_expression get_tech_failure h_low_depth_flag h_low_expression_flag h_tech_failure_flag |
| Checks Whether All Missing | all_na |
| Annotation Accessor and Setter | .row_data_annotation_cols annotation annotation,AnyHermesData-method annotation<-,AnyHermesData,DataFrame-method |
| Standard Assertion Arguments | assertion_arguments |
| Additional Assertions for 'assert_that' | assertions is_class is_constant is_counts_vector is_hermes_data is_list_with one_provided |
| All Standard Plots in Default Setting | autoplot,AnyHermesData-method plot_all |
| Principal Components Analysis Calculation | .HermesDataPca calc_pca HermesDataPca HermesDataPca-class |
| Concatenate and Print with Newline | cat_with_newline |
| Column Binding of 'AnyHermesData' Objects | cbind |
| Check for proportion | assert_proportion check_proportion expect_proportion test_proportion |
| Sample Variables with Selected Gene Information | col_data_with_genes |
| Mean Z-score Gene Signature | colMeanZscores |
| First Principal Component (PC1) Gene Signature | colPrinComp1 |
| Connection to 'BioMart' | .ConnectionBiomart ConnectionBiomart ConnectionBiomart-class connect_biomart |
| Control Settings for Counts Normalization | control_normalize |
| Control for Specified Quality Flags | control_quality |
| Generic Function for Correlation Calculations | correlate |
| Correlation between Sample Counts of 'AnyHermesData' | .HermesDataCor autoplot,HermesDataCor-method calc_cor correlate,AnyHermesData-method HermesDataCor HermesDataCor-class |
| Correlation of Principal Components with Sample Variables | .HermesDataPcaCor autoplot,HermesDataPcaCor-method correlate,HermesDataPca-method HermesDataPcaCor HermesDataPcaCor-class pca_cor_samplevar |
| Counts Accessor and Setter | counts counts,AnyHermesData-method counts<-,AnyHermesData,matrix-method |
| Cutting a Numeric Vector into a Factor of Quantile Bins | cut_quantile |
| Conversion of Eligible Columns to Factor Variables in a 'DataFrame' | df_cols_to_factor |
| Differential Expression Analysis | .HermesDataDiffExpr autoplot,HermesDataDiffExpr-method diff_expression HermesDataDiffExpr HermesDataDiffExpr-class |
| Barplot for Gene Expression Percentiles | draw_barplot |
| Boxplot for Gene Expression Values | draw_boxplot h_draw_boxplot_df |
| Stacked Barplot of Low Expression Genes by Chromosome | draw_genes_barplot |
| Heatmap for Gene Expression Counts | draw_heatmap |
| Density Plot of (Log) Counts Distributions | draw_libsize_densities |
| Histogram of Library Sizes | draw_libsize_hist |
| Q-Q Plot of Library Sizes | draw_libsize_qq |
| Boxplot of Non-Zero Genes | draw_nonzero_boxplot |
| Scatterplot for Gene Expression Values | draw_scatterplot |
| Example 'ExpressionSet' Data | expression_set |
| Extra Variable Names Accessor Methods | extraColDataNames extraColDataNames,AnyHermesData-method extraRowDataNames extraRowDataNames,AnyHermesData-method extra_data_names |
| Filter 'AnyHermesData' on Subset Passing Default QC Flags | filter filter,AnyHermesData-method filter,data.frame-method filter,ts-method |
| 'GeneSpec' Constructor | gene_spec |
| Gene IDs Accessor | genes genes,AnyHermesData-method |
| R6 Class Representing a Gene (Signature) Specification | GeneSpec |
| Finding All Duplicates in Vector | h_all_duplicated |
| Conversion to Factors with Explicit Missing Level in a 'data.frame' | h_df_factors_with_explicit_na |
| 'DESeq2' Differential Expression Analysis | h_diff_expr_deseq2 |
| 'limma'/voom Differential Expression Analysis | h_diff_expr_voom |
| Translation of 'Ensembl' to 'Entrez' Gene IDs | h_ensembl_to_entrez_ids |
| Get Annotations from 'BioMart' | h_get_annotation_biomart |
| Conversion of 'BioMart' Coordinates into 'GRanges' | h_get_granges_by_id |
| Total Length of All Exons for Genes | h_get_size_biomart |
| Predicate for Required Annotations | h_has_req_annotations |
| Helper Function For Matching Map Values to Names | h_map_pos |
| Parenthesize a Character Vector | h_parens |
| Calculation of R2 Matrix between Sample Variables and Principal Components | h_pca_df_r2_matrix |
| Calculation of R2 between Sample Variable and Principal Components | h_pca_var_rsquared |
| Make a Short List of a Character Vector | h_short_list |
| Stripping Prefix from Gene IDs | h_strip_prefix |
| Creation of Unique Labels | h_unique_labels |
| Example 'HermesData' Data | hermes_data |
| 'HermesData' and 'RangedHermesData' | .HermesData .RangedHermesData AnyHermesData AnyHermesData-class HermesData HermesData-class HermesDataFromMatrix RangedHermesData RangedHermesData-class |
| Inner Joining a Genes with a CDISC Data Set | inner_join_cdisc |
| Checking for Empty 'SummarizedExperiment' | isEmpty isEmpty,SummarizedExperiment-method |
| 'lapply' method for 'MultiAssayExperiment' | lapply lapply,MultiAssayExperiment-method |
| Metadata Accessor and Setter | metadata |
| Example 'MultiAssayExperiment' Data | multi_assay_experiment |
| Normalization of 'AnyHermesData' Objects | h_cpm h_rlog h_rpkm h_tpm h_voom h_vst normalize normalize,AnyHermesData-method |
| Prefix Accessor | prefix |
| Query Gene Annotations from a Connection | query query,character,ConnectionBiomart-method |
| Row Binding of 'AnyHermesData' Objects | rbind |
| Renaming Contents of 'SummarizedExperiment' Objects | rename rename,data.frame-method rename,SummarizedExperiment-method |
| Sample IDs Accessor | samples samples,AnyHermesData-method |
| Set Technical Failure Flags | set_tech_failure |
| Show Method for 'AnyHermesData' Objects | show show,HermesData-method show,RangedHermesData-method |
| Subsetting 'AnyHermesData' Objects | subset |
| Example 'SummarizedExperiment' Data | summarized_experiment |
| Summary Method for 'AnyHermesData' Objects | .HermesDataSummary HermesDataSummary HermesDataSummary-class show,HermesDataSummary-method summary summary,AnyHermesData-method |
| Derivation of Top Genes | .HermesDataTopGenes autoplot,HermesDataTopGenes-method HermesDataTopGenes HermesDataTopGenes-class top_genes |
| Internal Helper Functions for Validation of 'AnyHermesData' Objects | validate validate_cols validate_col_data validate_counts validate_names validate_prefix validate_row_data |
| Wrap in MAE | wrap_in_mae |