| .describe_transcript_SE | Get DESCRIPTION from gene SYMBOL for Human and Mouse |
| 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 |
| as_matrix | Get matrix from tibble |
| as_SummarizedExperiment | as_SummarizedExperiment |
| as_SummarizedExperiment-method | as_SummarizedExperiment |
| cluster_elements | Get clusters of elements (e.g., samples or transcripts) |
| cluster_elements-method | Get clusters of elements (e.g., samples or transcripts) |
| 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 |
| describe_transcript-method | Get DESCRIPTION from gene SYMBOL for Human and Mouse |
| fill_missing_abundance | Fill transcript abundance if missing from sample-transcript pairs |
| get_bibliography | Produces the bibliography list of your workflow |
| get_bibliography-method | Produces the bibliography list of your workflow |
| get_X_cibersort | Get Cibersort reference data |
| identify_abundant | Identify abundant transcripts/genes |
| identify_abundant-method | Identify abundant transcripts/genes |
| 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 |
| keep_abundant | Filter to keep only abundant transcripts/genes |
| keep_abundant-method | keep_abundant |
| keep_abundant-method | keep_abundant |
| keep_variable | Keep variable transcripts |
| keep_variable-method | Keep variable transcripts |
| log10_reverse_trans | Log10 reverse transformation for ggplot2 |
| logit_trans | logit scale |
| 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 |
| quantile_normalise_abundance | Normalise by quantiles the counts of transcripts/genes |
| quantile_normalise_abundance-method | Normalise by quantiles the counts of transcripts/genes |
| 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 |
| resolve_complete_confounders_of_non_interest | Resolve Complete Confounders of Non-Interest |
| resolve_complete_confounders_of_non_interest-method | resolve_complete_confounders_of_non_interest |
| 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 |
| scale_abundance | Scale the counts of transcripts/genes |
| scale_abundance-method | Scale the counts of transcripts/genes |
| scale_x_log10_reverse | scale_x_log10_reverse |
| scale_y_log10_reverse | scale_y_log10_reverse |
| test_differential_abundance | Perform differential transcription testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2 |
| test_differential_abundance-method | Perform differential transcription testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2 |
| test_differential_expression | Perform differential expression testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2 |
| test_differential_expression-method | Perform differential expression testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2 |
| 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 |
| test_gene_rank | analyse gene rank with GSEA |
| test_gene_rank-method | analyse gene rank with GSEA |
| test_stratification_cellularity-method | test_stratification_cellularity |
| tximeta_summarizeToGene_object | Needed for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximeta |
| 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 |