GeneSpec                R6 Class Representing a Gene (Signature)
                        Specification
HermesData-class        'HermesData' and 'RangedHermesData'
add_quality_flags       Add Quality Flags
all_na                  Checks Whether All Missing
annotation,AnyHermesData-method
                        Annotation Accessor and Setter
assertion_arguments     Standard Assertion Arguments
assertions              Additional Assertions for 'assert_that'
autoplot,AnyHermesData-method
                        All Standard Plots in Default Setting
calc_pca                Principal Components Analysis Calculation
cat_with_newline        Concatenate and Print with Newline
cbind                   Column Binding of 'AnyHermesData' Objects
check_proportion        Check for proportion
colMeanZscores          Mean Z-score Gene Signature
colPrinComp1            First Principal Component (PC1) Gene Signature
col_data_with_genes     Sample Variables with Selected Gene Information
connect_biomart         Connection to 'BioMart'
control_normalize       Control Settings for Counts Normalization
control_quality         Control for Specified Quality Flags
correlate               Generic Function for Correlation Calculations
correlate,AnyHermesData-method
                        Correlation between Sample Counts of
                        'AnyHermesData'
correlate,HermesDataPca-method
                        Correlation of Principal Components with Sample
                        Variables
counts,AnyHermesData-method
                        Counts Accessor and Setter
cut_quantile            Cutting a Numeric Vector into a Factor of
                        Quantile Bins
df_cols_to_factor       Conversion of Eligible Columns to Factor
                        Variables in a 'DataFrame'
diff_expression         Differential Expression Analysis
draw_barplot            Barplot for Gene Expression Percentiles
draw_boxplot            Boxplot for Gene Expression Values
draw_genes_barplot      Stacked Barplot of Low Expression Genes by
                        Chromosome
draw_heatmap            Heatmap for Gene Expression Counts
draw_libsize_densities
                        Density Plot of (Log) Counts Distributions
draw_libsize_hist       Histogram of Library Sizes
draw_libsize_qq         Q-Q Plot of Library Sizes
draw_nonzero_boxplot    Boxplot of Non-Zero Genes
draw_scatterplot        Scatterplot for Gene Expression Values
expression_set          Example 'ExpressionSet' Data
extra_data_names        Extra Variable Names Accessor Methods
filter                  Filter 'AnyHermesData' on Subset Passing
                        Default QC Flags
gene_spec               'GeneSpec' Constructor
genes                   Gene IDs Accessor
h_all_duplicated        Finding All Duplicates in Vector
h_df_factors_with_explicit_na
                        Conversion to Factors with Explicit Missing
                        Level in a 'data.frame'
h_diff_expr_deseq2      'DESeq2' Differential Expression Analysis
h_diff_expr_voom        'limma'/voom Differential Expression Analysis
h_ensembl_to_entrez_ids
                        Translation of 'Ensembl' to 'Entrez' Gene IDs
h_get_annotation_biomart
                        Get Annotations from 'BioMart'
h_get_granges_by_id     Conversion of 'BioMart' Coordinates into
                        'GRanges'
h_get_size_biomart      Total Length of All Exons for Genes
h_has_req_annotations   Predicate for Required Annotations
h_map_pos               Helper Function For Matching Map Values to
                        Names
h_parens                Parenthesize a Character Vector
h_pca_df_r2_matrix      Calculation of R2 Matrix between Sample
                        Variables and Principal Components
h_pca_var_rsquared      Calculation of R2 between Sample Variable and
                        Principal Components
h_short_list            Make a Short List of a Character Vector
h_strip_prefix          Stripping Prefix from Gene IDs
h_unique_labels         Creation of Unique Labels
hermes-package          'hermes' Package
hermes_data             Example 'HermesData' Data
inner_join_cdisc        Inner Joining a Genes with a CDISC Data Set
isEmpty,SummarizedExperiment-method
                        Checking for Empty 'SummarizedExperiment'
lapply,MultiAssayExperiment-method
                        'lapply' method for 'MultiAssayExperiment'
metadata                Metadata Accessor and Setter
multi_assay_experiment
                        Example 'MultiAssayExperiment' Data
normalize,AnyHermesData-method
                        Normalization of 'AnyHermesData' Objects
prefix                  Prefix Accessor
query                   Query Gene Annotations from a Connection
rbind                   Row Binding of 'AnyHermesData' Objects
rename,SummarizedExperiment-method
                        Renaming Contents of 'SummarizedExperiment'
                        Objects
samples,AnyHermesData-method
                        Sample IDs Accessor
set_tech_failure        Set Technical Failure Flags
show,HermesData-method
                        Show Method for 'AnyHermesData' Objects
subset                  Subsetting 'AnyHermesData' Objects
summarized_experiment   Example 'SummarizedExperiment' Data
summary                 Summary Method for 'AnyHermesData' Objects
top_genes               Derivation of Top Genes
validate                Internal Helper Functions for Validation of
                        'AnyHermesData' Objects
wrap_in_mae             Wrap in MAE
