API for insightsengineering/hermes
Preprocessing, analyzing, and reporting of RNA-seq data
| Global functions | |
|---|---|
| %>% | Man page |
| .ConnectionBiomart | Man page |
| .HermesData | Man page |
| .HermesDataCor | Man page |
| .HermesDataDiffExpr | Man page |
| .HermesDataPca | Man page |
| .HermesDataPcaCor | Man page |
| .HermesDataSummary | Man page |
| .HermesDataTopGenes | Man page |
| .RangedHermesData | Man page |
| .row_data_annotation_cols | Man page |
| .show.AnyHermesData | Source code |
| AnyHermesData | Man page |
| AnyHermesData-class | Man page |
| ConnectionBiomart | Man page |
| ConnectionBiomart-class | Man page |
| GeneSpec | Man page |
| HermesData | Man page Source code |
| HermesData-class | Man page |
| HermesDataCor | Man page |
| HermesDataCor-class | Man page |
| HermesDataDiffExpr | Man page |
| HermesDataDiffExpr-class | Man page |
| HermesDataFromMatrix | Man page Source code |
| HermesDataPca | Man page |
| HermesDataPca-class | Man page |
| HermesDataPcaCor | Man page |
| HermesDataPcaCor-class | Man page |
| HermesDataSummary | Man page |
| HermesDataSummary-class | Man page |
| HermesDataTopGenes | Man page |
| HermesDataTopGenes-class | Man page |
| RangedHermesData | Man page |
| RangedHermesData-class | Man page |
| add_quality_flags | Man page Source code |
| all_na | Man page Source code |
| annotation | Man page |
| annotation,AnyHermesData-method | Man page |
| annotation<-,AnyHermesData,DataFrame-method | Man page |
| assert_proportion | Man page |
| assertion_arguments | Man page |
| assertions | Man page |
| autoplot,AnyHermesData-method | Man page |
| autoplot,HermesDataCor-method | Man page |
| autoplot,HermesDataDiffExpr-method | Man page |
| autoplot,HermesDataPcaCor-method | Man page |
| autoplot,HermesDataTopGenes-method | Man page |
| calc_cor | Man page |
| calc_pca | Man page Source code |
| cat_with_newline | Man page Source code |
| cbind | Man page |
| check_proportion | Man page Source code |
| colMeanZscores | Man page Source code |
| colPrinComp1 | Man page Source code |
| col_data_with_genes | Man page Source code |
| connect_biomart | Man page Source code |
| control_normalize | Man page Source code |
| control_quality | Man page Source code |
| correlate | Man page |
| correlate,AnyHermesData-method | Man page |
| correlate,HermesDataPca-method | Man page |
| counts | Man page |
| counts,AnyHermesData-method | Man page |
| counts<-,AnyHermesData,matrix-method | Man page |
| cut_quantile | Man page Source code |
| df_cols_to_factor | Man page Source code |
| diff_expression | Man page Source code |
| draw_barplot | Man page Source code |
| draw_boxplot | Man page Source code |
| draw_genes_barplot | Man page Source code |
| draw_heatmap | Man page Source code |
| draw_libsize_densities | Man page Source code |
| draw_libsize_hist | Man page Source code |
| draw_libsize_qq | Man page Source code |
| draw_nonzero_boxplot | Man page Source code |
| draw_scatterplot | Man page Source code |
| expect_proportion | Man page |
| expression_set | Man page |
| extraColDataNames | Man page |
| extraColDataNames,AnyHermesData-method | Man page |
| extraRowDataNames | Man page |
| extraRowDataNames,AnyHermesData-method | Man page |
| extra_data_names | Man page |
| filter | Man page |
| filter,AnyHermesData-method | Man page |
| filter,data.frame-method | Man page |
| filter,ts-method | Man page |
| gene_spec | Man page Source code |
| genes | Man page |
| genes,AnyHermesData-method | Man page |
| get_low_depth | Man page Source code |
| get_low_expression | Man page Source code |
| get_tech_failure | Man page Source code |
| h_all_duplicated | Man page Source code |
| h_cpm | Man page Source code |
| h_df_factors_with_explicit_na | Man page Source code |
| h_diff_expr_deseq2 | Man page Source code |
| h_diff_expr_voom | Man page Source code |
| h_draw_boxplot_df | Man page Source code |
| h_ensembl_to_entrez_ids | Man page Source code |
| h_get_annotation_biomart | Man page Source code |
| h_get_granges_by_id | Man page Source code |
| h_get_size_biomart | Man page Source code |
| h_has_req_annotations | Man page Source code |
| h_low_depth_flag | Man page Source code |
| h_low_expression_flag | Man page Source code |
| h_map_pos | Man page Source code |
| h_parens | Man page Source code |
| h_pca_df_r2_matrix | Man page Source code |
| h_pca_var_rsquared | Man page Source code |
| h_rlog | Man page Source code |
| h_rpkm | Man page Source code |
| h_short_list | Man page Source code |
| h_strip_prefix | Man page Source code |
| h_tech_failure_flag | Man page Source code |
| h_tpm | Man page Source code |
| h_unique_labels | Man page Source code |
| h_voom | Man page Source code |
| h_vst | Man page Source code |
| hermes | Man page |
| hermes-package | Man page |
| hermes_data | Man page |
| inner_join_cdisc | Man page Source code |
| isEmpty | Man page |
| isEmpty,SummarizedExperiment-method | Man page |
| is_class | Man page Source code |
| is_constant | Man page Source code |
| is_counts_vector | Man page Source code |
| is_hermes_data | Man page Source code |
| is_list_with | Man page Source code |
| lapply | Man page |
| lapply,MultiAssayExperiment-method | Man page |
| metadata | Man page |
| multi_assay_experiment | Man page |
| normalize | Man page |
| normalize,AnyHermesData-method | Man page |
| one_provided | Man page Source code |
| pca_cor_samplevar | Man page |
| plot_all | Man page |
| prefix | Man page |
| query | Man page |
| query,character,ConnectionBiomart-method | Man page |
| rbind | Man page |
| rename | Man page |
| rename,SummarizedExperiment-method | Man page |
| rename,data.frame-method | Man page |
| samples | Man page |
| samples,AnyHermesData-method | Man page |
| set_tech_failure | Man page Source code |
| show | Man page |
| show,HermesData-method | Man page |
| show,HermesDataSummary-method | Man page |
| show,RangedHermesData-method | Man page |
| subset | Man page |
| summarized_experiment | Man page |
| summary | Man page |
| summary,AnyHermesData-method | Man page |
| test_proportion | Man page |
| top_genes | Man page Source code |
| validate | Man page |
| validate_col_data | Man page Source code |
| validate_cols | Man page Source code |
| validate_counts | Man page Source code |
| validate_names | Man page Source code |
| validate_prefix | Man page Source code |
| validate_row_data | Man page Source code |
| wrap_in_mae | Man page Source code |
