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| adjust_abundance | Adjust transcript abundance for unwanted variation |
| adjust_abundance-method | Adjust transcript abundance for unwanted variation |
| aggregate_duplicates | Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columns |
| aggregate_duplicates-method | Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columns |
| arrange | drplyr-methods |
| arrange.default | drplyr-methods |
| as_matrix | Get matrix from tibble |
| bind | Efficiently bind multiple data frames by row and column |
| bind_cols | drplyr-methods |
| bind_rows | drplyr-methods |
| breast_tcga_mini | Data set |
| cluster_elements | Get clusters of elements (e.g., samples or transcripts) |
| cluster_elements-method | Get clusters of elements (e.g., samples or transcripts) |
| counts | Example data set |
| counts_ensembl | Counts with ensembl annotation |
| counts_mini | Example data set reduced |
| deconvolve_cellularity | Get cell type proportions from samples |
| deconvolve_cellularity-method | Get cell type proportions from samples |
| describe_transcript | Get DESCRIPTION from gene SYMBOL for Human and Mouse |
| distinct | distinct |
| ensembl_symbol_mapping | Data set |
| ensembl_to_symbol | Add transcript symbol column from ensembl id for human and mouse data |
| ensembl_to_symbol-method | Add transcript symbol column from ensembl id for human and mouse data |
| fill_missing_abundance | Fill transcript abundance if missing from sample-transcript pairs |
| fill_missing_abundance-method | Fill transcript abundance if missing from sample-transcript pairs |
| filter | Subset rows using column values |
| flybaseIDs | flybaseIDs |
| full_join | Full join datasets |
| get_bibliography | Produces the bibliography list of your workflow |
| get_bibliography-method | Produces the bibliography list of your workflow |
| group_by | Group by one or more variables |
| identify_abundant | find abundant transcripts |
| identify_abundant-method | find abundant transcripts |
| impute_missing_abundance | impute transcript abundance if missing from sample-transcript pairs |
| impute_missing_abundance-method | impute transcript abundance if missing from sample-transcript pairs |
| inner_join | Inner join datasets |
| keep_abundant | Keep abundant transcripts |
| keep_abundant-method | Keep abundant transcripts |
| keep_variable | Keep variable transcripts |
| keep_variable-method | Keep variable transcripts |
| left_join | Left join datasets |
| log10_reverse_trans | log10_reverse_trans |
| logit_trans | logit scale |
| mutate | Create, modify, and delete columns |
| nest | unnest |
| nest.default | unnest |
| nest.tidybulk | unnest |
| parse_formula_survival | Formula parser with survival |
| pivot_sample | Extract sample-wise information |
| pivot_sample-method | Extract sample-wise information |
| pivot_transcript | Extract transcript-wise information |
| pivot_transcript-method | Extract transcript-wise information |
| reduce_dimensions | Dimension reduction of the transcript abundance data |
| reduce_dimensions-method | Dimension reduction of the transcript abundance data |
| remove_redundancy | Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) abundances are correlated |
| remove_redundancy-method | Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) abundances are correlated |
| rename | Rename columns |
| right_join | Right join datasets |
| rotate_dimensions | Rotate two dimensions (e.g., principal components) of an arbitrary angle |
| rotate_dimensions-method | Rotate two dimensions (e.g., principal components) of an arbitrary angle |
| rowwise | Group input by rows |
| scale_abundance | Scale the counts of transcripts/genes |
| scale_abundance-method | Scale the counts of transcripts/genes |
| se | SummarizedExperiment |
| se_mini | SummarizedExperiment mini for vignette |
| summarise | Summarise each group to fewer rows |
| symbol_to_entrez | Get ENTREZ id from gene SYMBOL |
| test_deseq2_df | SummarizedExperiment mini for vignette |
| test_differential_abundance | Perform differential transcription testing using edgeR QLT, edgeR LR, limma-voom or DESeq2 |
| test_differential_abundance-method | Perform differential transcription testing using edgeR QLT, edgeR LR, limma-voom or DESeq2 |
| test_differential_cellularity | Add differential tissue composition information to a tbl |
| test_differential_cellularity-method | Add differential tissue composition information to a tbl |
| test_gene_enrichment | analyse gene enrichment with EGSEA |
| test_gene_enrichment-method | analyse gene enrichment with EGSEA |
| test_gene_overrepresentation | analyse gene over-representation with GSEA |
| test_gene_overrepresentation-method | analyse gene over-representation with GSEA |
| tidybulk | Creates a 'tt' object from a 'tbl' or 'SummarizedExperiment' object |
| tidybulk-method | Creates a 'tt' object from a 'tbl' or 'SummarizedExperiment' object |
| tidybulk_SAM_BAM | Creates a 'tt' object from a list of file names of BAM/SAM |
| tidybulk_SAM_BAM-method | Creates a 'tt' object from a list of file names of BAM/SAM |
| ungroup | drplyr-methods |
| unnest | unnest |
| unnest.default | unnest |
| unnest.nested_tidybulk | unnest |
| vignette_manuscript_signature_boxplot | Needed for vignette vignette_manuscript_signature_boxplot |
| vignette_manuscript_signature_tsne | Needed for vignette vignette_manuscript_signature_tsne |
| vignette_manuscript_signature_tsne2 | Needed for vignette vignette_manuscript_signature_tsne2 |
| X_cibersort | Cibersort reference |