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