| %>% |
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
|
