Man pages for insightsengineering/hermes
Preprocessing, analyzing, and reporting of RNA-seq data

all_naChecks Whether All Missing
annotationAnnotation Accessor and Setter
assertion_argumentsStandard Assertion Arguments
assertionsAdditional Assertions for 'assert_that'
calc_corCorrelation between Sample Counts of 'AnyHermesData'
calc_pcaPrincipal Components Analysis Calculation
cat_with_newlineConcatenate and Print with Newline
cbindColumn Binding of 'AnyHermesData' Objects
check_proportionCheck for proportion
col_data_with_genesSample Variables with Selected Gene Information
colMeanZscoresMean Z-score Gene Signature
colPrinComp1First Principal Component (PC1) Gene Signature
connect_biomartConnection to BioMart
control_normalizeControl Settings for Counts Normalization
control_qualityControl for Specified Quality Flags
correlateGeneric Function for Correlation Calculations
countsCounts Accessor and Setter
cut_quantileCutting a Numeric Vector into a Factor of Quantile Bins
df_cols_to_factorConversion of Eligible Columns to Factor Variables in a...
diff_expressionDifferential Expression Analysis
draw_barplotBarplot for Gene Expression Percentiles
draw_boxplotBoxplot for Gene Expression Values
draw_genes_barplotStacked Barplot of Low Expression Genes by Chromosome
draw_heatmapHeatmap for Gene Expression Counts
draw_libsize_densitiesDensity Plot of (Log) Counts Distributions
draw_libsize_histHistogram of Library Sizes
draw_libsize_qqQ-Q Plot of Library Sizes
draw_nonzero_boxplotBoxplot of Non-Zero Genes
draw_scatterplotScatterplot for Gene Expression Values
expression_setExample 'ExpressionSet' Data
extra_data_namesExtra Variable Names Accessor Methods
filterFilter 'AnyHermesData' on Subset Passing Default QC Flags
genesGene IDs Accessor
gene_spec'GeneSpec' Constructor
GeneSpecR6 Class Representing a Gene (Signature) Specification
h_all_duplicatedFinding All Duplicates in Vector
h_df_factors_with_explicit_naConversion to Factors with Explicit Missing Level in a...
h_diff_expr_deseq2DESeq2 Differential Expression Analysis
h_diff_expr_voom'limma'/'voom' Differential Expression Analysis
h_ensembl_to_entrez_idsTranslation of Ensembl to Entrez Gene IDs
hermes_dataExample 'HermesData' Data
HermesData-class'HermesData' and 'RangedHermesData'
hermes-package'hermes' Package
h_get_annotation_biomartGet Annotations from BioMart
h_get_granges_by_idConversion of BioMart Coordinates into 'GRanges'
h_get_size_biomartTotal Length of All Exons for Genes
h_has_req_annotationsPredicate for Required Annotations
h_map_posHelper Function For Matching Map Values to Names
h_parensParenthesize a Character Vector
h_pca_df_r2_matrixCalculation of R2 Matrix between Sample Variables and...
h_pca_var_rsquaredCalculation of R2 between Sample Variable and Principal...
h_short_listMake a Short List of a Character Vector
h_strip_prefixStripping Prefix from Gene IDs
h_unique_labelsCreation of Unique Labels
inner_join_cdiscInner Joining a Genes with a CDISC Data Set
isEmptyChecking for Empty 'SummarizedExperiment'
lapply'lapply' method for 'MultiAssayExperiment'
metadataMetadata Accessor and Setter
multi_assay_experimentExample 'MultiAssayExperiment' Data
normalizeNormalization of 'AnyHermesData' Objects
pca_cor_samplevarCorrelation of Principal Components with Sample Variables
pipePipe operator
plot_allAll Standard Plots in Default Setting
prefixPrefix Accessor
quality_flagsAdd Quality Flags
queryQuery Gene Annotations from a Connection
rbindRow Binding of 'AnyHermesData' Objects
renameRenaming Contents of 'SummarizedExperiment' Objects
samplesSample IDs Accessor
set_tech_failureSet Technical Failure Flags
showShow Method for 'AnyHermesData' Objects
subsetSubsetting 'AnyHermesData' Objects
summarized_experimentExample 'SummarizedExperiment' Data
summarySummary Method for 'AnyHermesData' Objects
top_genesDerivation of Top Genes
validateInternal Helper Functions for Validation of 'AnyHermesData'...
wrap_in_maeWrap in MAE
insightsengineering/hermes documentation built on March 1, 2023, 5:58 a.m.