add_attr	add_attr
add_class	add_class
add_scaled_counts_bulk.calcNormFactor	add_scaled_counts_bulk.calcNormFactor
add_scaled_counts_bulk.get_low_expressed	add_scaled_counts_bulk.get_low_expressed
adjust_abundance	adjust_abundance-methods
adjust_abundance,RangedSummarizedExperiment-method	adjust_abundance-methods
adjust_abundance,spec_tbl_df-method	adjust_abundance-methods
adjust_abundance,SummarizedExperiment-method	adjust_abundance-methods
adjust_abundance,tbl_df-method	adjust_abundance-methods
adjust_abundance,tidybulk-method	adjust_abundance-methods
aggregate_duplicated_transcripts_bulk	aggregate_duplicated_transcripts_bulk
aggregate_duplicates	aggregate_duplicates-methods
aggregate_duplicates,RangedSummarizedExperiment-method	aggregate_duplicates-methods
aggregate_duplicates,spec_tbl_df-method	aggregate_duplicates-methods
aggregate_duplicates,SummarizedExperiment-method	aggregate_duplicates-methods
aggregate_duplicates,tbl_df-method	aggregate_duplicates-methods
aggregate_duplicates,tidybulk-method	aggregate_duplicates-methods
arrange	dplyr-methods
arrange.default	dplyr-methods
as_matrix	as_matrix
as_tibble	reexports
bind	bind
bind_cols	dplyr-methods
bind_rows	dplyr-methods
breast_tcga_mini	breast_tcga_mini
check_if_counts_is_na	check_if_counts_is_na
check_if_duplicated_genes	check_if_duplicated_genes
check_if_wrong_input	check_if_wrong_input
cluster_elements	cluster_elements-methods
cluster_elements,RangedSummarizedExperiment-method	cluster_elements-methods
cluster_elements,spec_tbl_df-method	cluster_elements-methods
cluster_elements,SummarizedExperiment-method	cluster_elements-methods
cluster_elements,tbl_df-method	cluster_elements-methods
cluster_elements,tidybulk-method	cluster_elements-methods
counts	counts
counts_ensembl	counts_ensembl
counts_mini	counts_mini
create_tt_from_bam_sam_bulk	create_tt_from_bam_sam_bulk
create_tt_from_tibble_bulk	create_tt_from_tibble_bulk
deconvolve_cellularity	deconvolve_cellularity-methods
deconvolve_cellularity,RangedSummarizedExperiment-method	deconvolve_cellularity-methods
deconvolve_cellularity,spec_tbl_df-method	deconvolve_cellularity-methods
deconvolve_cellularity,SummarizedExperiment-method	deconvolve_cellularity-methods
deconvolve_cellularity,tbl_df-method	deconvolve_cellularity-methods
deconvolve_cellularity,tidybulk-method	deconvolve_cellularity-methods
distinct	distinct
do	reexports
drop_attr	drop_attr
drop_class	drop_class
ensembl_symbol_mapping	ensembl_symbol_mapping
ensembl_to_symbol	ensembl_to_symbol-methods
ensembl_to_symbol,spec_tbl_df-method	ensembl_to_symbol-methods
ensembl_to_symbol,tbl_df-method	ensembl_to_symbol-methods
ensembl_to_symbol,tidybulk-method	ensembl_to_symbol-methods
error_if_counts_is_na	error_if_counts_is_na
error_if_duplicated_genes	error_if_duplicated_genes
error_if_log_transformed	error_if_log_transformed
error_if_wrong_input	error_if_wrong_input
fill_NA_using_formula	fill_NA_using_formula
fill_NA_with_row_median	fill_NA_with_row_median
filter	filter
flybaseIDs	flybaseIDs
full_join	full_join
get_abundance_norm_if_exists	get_abundance_norm_if_exists
get_adjusted_counts_for_unwanted_variation_bulk	get_adjusted_counts_for_unwanted_variation_bulk
get_cell_type_proportions	get_cell_type_proportions
get_clusters_kmeans_bulk	get_clusters_kmeans_bulk
get_clusters_SNN_bulk	get_clusters_SNN_bulk
get_differential_transcript_abundance_bulk	get_differential_transcript_abundance_bulk
get_elements	get_elements
get_elements_features	get_elements_features
get_elements_features_abundance	get_elements_features_abundance
get_reduced_dimensions_MDS_bulk	get_reduced_dimensions_MDS_bulk
get_reduced_dimensions_PCA_bulk	get_reduced_dimensions_PCA_bulk
get_reduced_dimensions_TSNE_bulk	get_reduced_dimensions_TSNE_bulk
get_rotated_dimensions	get_rotated_dimensions
get_sample	get_sample
get_sample_counts	get_sample_counts
get_sample_transcript	get_sample_transcript
get_sample_transcript_counts	get_sample_transcript_counts
get_scaled_counts_bulk	get_scaled_counts_bulk
get_symbol_from_ensembl	get_symbol_from_ensembl
get_transcript	get_transcript
get_x_y_annotation_columns	get_x_y_annotation_columns
group_by	group_by
ifelse2_pipe	ifelse2_pipe
ifelse_pipe	ifelse_pipe
impute_abundance	impute_abundance-methods
impute_abundance,RangedSummarizedExperiment-method	impute_abundance-methods
impute_abundance,spec_tbl_df-method	impute_abundance-methods
impute_abundance,SummarizedExperiment-method	impute_abundance-methods
impute_abundance,tbl_df-method	impute_abundance-methods
impute_abundance,tidybulk-method	impute_abundance-methods
inner_join	inner_join
keep_abundant	keep_abundant-methods
keep_abundant,RangedSummarizedExperiment-method	keep_abundant-methods
keep_abundant,spec_tbl_df-method	keep_abundant-methods
keep_abundant,SummarizedExperiment-method	keep_abundant-methods
keep_abundant,tbl_df-method	keep_abundant-methods
keep_abundant,tidybulk-method	keep_abundant-methods
keep_variable	keep_variable-methods
keep_variable,RangedSummarizedExperiment-method	keep_variable-methods
keep_variable,spec_tbl_df-method	keep_variable-methods
keep_variable,SummarizedExperiment-method	keep_variable-methods
keep_variable,tbl_df-method	keep_variable-methods
keep_variable,tidybulk-method	keep_variable-methods
keep_variable_transcripts	keep_variable_transcripts
left_join	left_join
mutate	mutate
nest	tidyr-methods
nest.default	tidyr-methods
nest.tidybulk	tidyr-methods
parse_formula	parse_formula
pivot_sample	pivot_sample-methods
pivot_sample,spec_tbl_df-method	pivot_sample-methods
pivot_sample,tbl_df-method	pivot_sample-methods
pivot_sample,tidybulk-method	pivot_sample-methods
pivot_transcript	pivot_transcript-methods
pivot_transcript,spec_tbl_df-method	pivot_transcript-methods
pivot_transcript,tbl_df-method	pivot_transcript-methods
pivot_transcript,tidybulk-method	pivot_transcript-methods
prepend	prepend
reduce_dimensions	reduce_dimensions-methods
reduce_dimensions,RangedSummarizedExperiment-method	reduce_dimensions-methods
reduce_dimensions,spec_tbl_df-method	reduce_dimensions-methods
reduce_dimensions,SummarizedExperiment-method	reduce_dimensions-methods
reduce_dimensions,tbl_df-method	reduce_dimensions-methods
reduce_dimensions,tidybulk-method	reduce_dimensions-methods
reexports	reexports
remove_redundancy	remove_redundancy-methods
remove_redundancy,RangedSummarizedExperiment-method	remove_redundancy-methods
remove_redundancy,spec_tbl_df-method	remove_redundancy-methods
remove_redundancy,SummarizedExperiment-method	remove_redundancy-methods
remove_redundancy,tbl_df-method	remove_redundancy-methods
remove_redundancy,tidybulk-method	remove_redundancy-methods
remove_redundancy_elements_though_reduced_dimensions	remove_redundancy_elements_though_reduced_dimensions
remove_redundancy_elements_through_correlation	remove_redundancy_elements_through_correlation
rename	rename
right_join	right_join
rotate_dimensions	rotate_dimensions-methods
rotate_dimensions,RangedSummarizedExperiment-method	rotate_dimensions-methods
rotate_dimensions,spec_tbl_df-method	rotate_dimensions-methods
rotate_dimensions,SummarizedExperiment-method	rotate_dimensions-methods
rotate_dimensions,tbl_df-method	rotate_dimensions-methods
rotate_dimensions,tidybulk-method	rotate_dimensions-methods
rowwise	rowwise
run_llsr	run_llsr
scale_abundance	scale_abundance-methods
scale_abundance,RangedSummarizedExperiment-method	scale_abundance-methods
scale_abundance,spec_tbl_df-method	scale_abundance-methods
scale_abundance,SummarizedExperiment-method	scale_abundance-methods
scale_abundance,tbl_df-method	scale_abundance-methods
scale_abundance,tidybulk-method	scale_abundance-methods
scale_design	scale_design
se	se
select_closest_pairs	select_closest_pairs
se_mini	se_mini
summarise	summarise
symbol_to_entrez	symbol_to_entrez
test_differential_abundance	test_differential_abundance-methods
test_differential_abundance,RangedSummarizedExperiment-method	test_differential_abundance-methods
test_differential_abundance,spec_tbl_df-method	test_differential_abundance-methods
test_differential_abundance,SummarizedExperiment-method	test_differential_abundance-methods
test_differential_abundance,tbl_df-method	test_differential_abundance-methods
test_differential_abundance,tidybulk-method	test_differential_abundance-methods
test_gene_enrichment	test_gene_enrichment-methods
test_gene_enrichment,spec_tbl_df-method	test_gene_enrichment-methods
test_gene_enrichment,tbl_df-method	test_gene_enrichment-methods
test_gene_enrichment,tidybulk-method	test_gene_enrichment-methods
test_gene_enrichment_bulk_EGSEA	test_gene_enrichment_bulk_EGSEA
test_gene_overrepresentation	test_gene_overrepresentation-methods
test_gene_overrepresentation,spec_tbl_df-method	test_gene_overrepresentation-methods
test_gene_overrepresentation,tbl_df-method	test_gene_overrepresentation-methods
test_gene_overrepresentation,tidybulk-method	test_gene_overrepresentation-methods
tibble	reexports
tidybulk	tidybulk-methods
tidybulk,RangedSummarizedExperiment-method	tidybulk-methods
tidybulk,spec_tbl_df-method	tidybulk-methods
tidybulk,SummarizedExperiment-method	tidybulk-methods
tidybulk,tbl_df-method	tidybulk-methods
tidybulk_SAM_BAM	tidybulk_SAM_BAM-methods
tidybulk_SAM_BAM,character,character-method	tidybulk_SAM_BAM-methods
tidybulk_to_SummarizedExperiment	tidybulk_to_SummarizedExperiment
ungroup	dplyr-methods
X_cibersort	X_cibersort
