API for stemangiola/tidyBulk
Brings transcriptomics to the tidyverse

Global functions
%>% Man page
.scale_abundance Source code
.tidybulk Source code
.tidybulk_se Source code
CoreAlg Source code
X_cibersort Man page
add_attr Man page
add_class Man page
add_scaled_counts_bulk.calcNormFactor Man page
add_scaled_counts_bulk.get_low_expressed Man page
adjust_abundance Man page
adjust_abundance,RangedSummarizedExperiment-method Man page
adjust_abundance,SummarizedExperiment-method Man page
adjust_abundance,spec_tbl_df-method Man page
adjust_abundance,tbl_df-method Man page
adjust_abundance,tidybulk-method Man page
aggregate_duplicated_transcripts_bulk Man page
aggregate_duplicates Man page
aggregate_duplicates,RangedSummarizedExperiment-method Man page
aggregate_duplicates,SummarizedExperiment-method Man page
aggregate_duplicates,spec_tbl_df-method Man page
aggregate_duplicates,tbl_df-method Man page
aggregate_duplicates,tidybulk-method Man page
arrange Man page Source code
arrange.default Man page Source code
arrange.tidybulk Source code
as_matrix Man page
as_tibble Man page
bind Man page
bind_cols Man page Source code
bind_cols.default Source code
bind_cols.tidybulk Source code
bind_rows Man page Source code
bind_rows.default Source code
bind_rows.tidybulk Source code
breast_tcga_mini Man page
check_if_attribute_present Source code
check_if_column_missing Source code
check_if_counts_is_na Man page Source code
check_if_data_rectangular Source code
check_if_duplicated_genes Man page Source code
check_if_transcript_is_na Source code
check_if_wrong_input Man page Source code
cluster_elements Man page
cluster_elements,RangedSummarizedExperiment-method Man page
cluster_elements,SummarizedExperiment-method Man page
cluster_elements,spec_tbl_df-method Man page
cluster_elements,tbl_df-method Man page
cluster_elements,tidybulk-method Man page
column_type_checking Source code
counts Man page
counts_ensembl Man page
counts_mini Man page
create_tt_from_bam_sam_bulk Man page Source code
create_tt_from_tibble_bulk Man page Source code
deconvolve_cellularity Man page
deconvolve_cellularity,RangedSummarizedExperiment-method Man page
deconvolve_cellularity,SummarizedExperiment-method Man page
deconvolve_cellularity,spec_tbl_df-method Man page
deconvolve_cellularity,tbl_df-method Man page
deconvolve_cellularity,tidybulk-method Man page
describe_transcript Man page
distinct Man page
do Man page
doPerm Source code
drop_attr Man page
drop_class Man page
eliminate_sparse_transcripts Source code
ensembl_symbol_mapping Man page
ensembl_to_symbol Man page
ensembl_to_symbol,spec_tbl_df-method Man page
ensembl_to_symbol,tbl_df-method Man page
ensembl_to_symbol,tidybulk-method Man page
error_if_counts_is_na Man page Source code
error_if_data_is_not_rectangular Source code
error_if_duplicated_genes Man page Source code
error_if_log_transformed Man page Source code
error_if_wrong_input Man page Source code
fill_NA_using_formula Man page
fill_NA_using_value Man page
fill_NA_with_row_median Man page
fill_missing_abundance Man page
fill_missing_abundance,RangedSummarizedExperiment-method Man page
fill_missing_abundance,SummarizedExperiment-method Man page
fill_missing_abundance,spec_tbl_df-method Man page
fill_missing_abundance,tbl_df-method Man page
fill_missing_abundance,tidybulk-method Man page
filter Man page
flybaseIDs Man page
full_join Man page
get_abundance_norm_if_exists Man page
get_adjusted_counts_for_unwanted_variation_bulk Man page
get_bibliography Man page
get_bibliography,tidybulk-method Man page
get_cell_type_proportions Man page
get_clusters_SNN_bulk Man page
get_clusters_kmeans_bulk Man page
get_differential_transcript_abundance_bulk Man page
get_differential_transcript_abundance_bulk_voom Man page
get_differential_transcript_abundance_deseq2 Man page
get_elements Man page
get_elements_features Man page
get_elements_features_abundance Man page
get_reduced_dimensions_MDS_bulk Man page
get_reduced_dimensions_PCA_bulk Man page
get_reduced_dimensions_TSNE_bulk Man page
get_rotated_dimensions Man page
get_sample Man page
get_sample_counts Man page
get_sample_transcript Man page
get_sample_transcript_counts Man page
get_scaled_counts_bulk Man page
get_symbol_from_ensembl Man page
get_transcript Man page
get_x_y_annotation_columns Man page
group_by Man page
identify_abundant Man page
identify_abundant,RangedSummarizedExperiment-method Man page
identify_abundant,SummarizedExperiment-method Man page
identify_abundant,spec_tbl_df-method Man page
identify_abundant,tbl_df-method Man page
identify_abundant,tidybulk-method Man page
ifelse2_pipe Man page Source code
ifelse_pipe Man page Source code
impute_missing_abundance Man page
impute_missing_abundance,RangedSummarizedExperiment-method Man page
impute_missing_abundance,SummarizedExperiment-method Man page
impute_missing_abundance,spec_tbl_df-method Man page
impute_missing_abundance,tbl_df-method Man page
impute_missing_abundance,tidybulk-method Man page
inner_join Man page
keep_abundant Man page
keep_abundant,RangedSummarizedExperiment-method Man page
keep_abundant,SummarizedExperiment-method Man page
keep_abundant,spec_tbl_df-method Man page
keep_abundant,tbl_df-method Man page
keep_abundant,tidybulk-method Man page
keep_variable Man page
keep_variable,RangedSummarizedExperiment-method Man page
keep_variable,SummarizedExperiment-method Man page
keep_variable,spec_tbl_df-method Man page
keep_variable,tbl_df-method Man page
keep_variable,tidybulk-method Man page
keep_variable_transcripts Man page
left_join Man page
log10_reverse_trans Man page
logit_trans Man page
mutate Man page Source code
mutate.default Source code
mutate.nested_tidybulk Source code
mutate.tidybulk Source code
my_CIBERSORT Source code
my_bibliography Source code
my_stop Source code
nest Man page
nest.default Man page
nest.tidybulk Man page
parse_formula Man page Source code
parse_formula_survival Man page Source code
pivot_sample Man page
pivot_sample,spec_tbl_df-method Man page
pivot_sample,tbl_df-method Man page
pivot_sample,tidybulk-method Man page
pivot_transcript Man page
pivot_transcript,spec_tbl_df-method Man page
pivot_transcript,tbl_df-method Man page
pivot_transcript,tidybulk-method Man page
prepend Man page
quo_names Man page
reduce_dimensions Man page
reduce_dimensions,RangedSummarizedExperiment-method Man page
reduce_dimensions,SummarizedExperiment-method Man page
reduce_dimensions,spec_tbl_df-method Man page
reduce_dimensions,tbl_df-method Man page
reduce_dimensions,tidybulk-method Man page
reexports Man page
remove_redundancy Man page
remove_redundancy,RangedSummarizedExperiment-method Man page
remove_redundancy,SummarizedExperiment-method Man page
remove_redundancy,spec_tbl_df-method Man page
remove_redundancy,tbl_df-method Man page
remove_redundancy,tidybulk-method Man page
remove_redundancy_elements_though_reduced_dimensions Man page
remove_redundancy_elements_through_correlation Man page
rename Man page Source code
rename.default Source code
rename.tidybulk Source code
right_join Man page
rotate_dimensions Man page
rotate_dimensions,RangedSummarizedExperiment-method Man page
rotate_dimensions,SummarizedExperiment-method Man page
rotate_dimensions,spec_tbl_df-method Man page
rotate_dimensions,tbl_df-method Man page
rotate_dimensions,tidybulk-method Man page
rowwise Man page Source code
rowwise.default Source code
rowwise.tidybulk Source code
run_epic Man page
run_llsr Man page
scale_abundance Man page
scale_abundance,RangedSummarizedExperiment-method Man page
scale_abundance,SummarizedExperiment-method Man page
scale_abundance,spec_tbl_df-method Man page
scale_abundance,tbl_df-method Man page
scale_abundance,tidybulk-method Man page
scale_design Man page Source code
se Man page
se_mini Man page
select_closest_pairs Man page
summarise Man page
symbol_to_entrez Man page
test_deseq2_df Man page
test_differential_abundance Man page
test_differential_abundance,RangedSummarizedExperiment-method Man page
test_differential_abundance,SummarizedExperiment-method Man page
test_differential_abundance,spec_tbl_df-method Man page
test_differential_abundance,tbl_df-method Man page
test_differential_abundance,tidybulk-method Man page
test_differential_cellularity Man page
test_differential_cellularity,RangedSummarizedExperiment-method Man page
test_differential_cellularity,SummarizedExperiment-method Man page
test_differential_cellularity,spec_tbl_df-method Man page
test_differential_cellularity,tbl_df-method Man page
test_differential_cellularity,tidybulk-method Man page
test_differential_cellularity_ Man page
test_gene_enrichment Man page
test_gene_enrichment,spec_tbl_df-method Man page
test_gene_enrichment,tbl_df-method Man page
test_gene_enrichment,tidybulk-method Man page
test_gene_enrichment_bulk_EGSEA Man page
test_gene_overrepresentation Man page
test_gene_overrepresentation,spec_tbl_df-method Man page
test_gene_overrepresentation,tbl_df-method Man page
test_gene_overrepresentation,tidybulk-method Man page
tibble Man page
tidybulk Man page
tidybulk,RangedSummarizedExperiment-method Man page
tidybulk,SummarizedExperiment-method Man page
tidybulk,spec_tbl_df-method Man page
tidybulk,tbl_df-method Man page
tidybulk_SAM_BAM Man page
tidybulk_SAM_BAM,character,character-method Man page
tidybulk_to_SummarizedExperiment Man page
tidybulk_to_tbl Source code
ungroup Man page Source code
unnest Man page
unnest.default Man page
unnest.nested_tidybulk Man page
validation Source code
validation.tidybulk Source code
validation_default Source code
vignette_manuscript_signature_boxplot Man page
vignette_manuscript_signature_tsne Man page
vignette_manuscript_signature_tsne2 Man page
warning_if_data_is_not_rectangular Source code
stemangiola/tidyBulk documentation built on Dec. 10, 2020, 8:20 a.m.