X_cibersort Cibersort reference adjust_abundance 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 arrange Arrange rows by column values as_SummarizedExperiment as_SummarizedExperiment as_matrix Get matrix from tibble bind Efficiently bind multiple data frames by row and column breast_tcga_mini_SE Needed for vignette breast_tcga_mini_SE cluster_elements Get clusters of elements (e.g., samples or transcripts) counts_SE Needed for vignette counts_SE counts_ensembl Counts with ensembl annotation deconvolve_cellularity 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 fill_missing_abundance Fill transcript abundance if missing from sample-transcript pairs filter Subset rows using column values flybaseIDs flybaseIDs get_bibliography Produces the bibliography list of your workflow group_by Group by one or more variables identify_abundant find abundant transcripts impute_missing_abundance impute transcript abundance if missing from sample-transcript pairs inner_join Inner join datasets keep_abundant Keep abundant transcripts keep_variable Keep variable transcripts left_join Left join datasets log10_reverse_trans log10_reverse_trans logit_trans logit scale mutate Create, modify, and delete columns pivot_sample Extract sample-wise information pivot_transcript Extract transcript-wise information reduce_dimensions 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 rename Rename columns rotate_dimensions Rotate two dimensions (e.g., principal components) of an arbitrary angle rowwise Group input by rows scale_abundance 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 quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2 test_differential_cellularity Add differential tissue composition information to a tbl test_gene_enrichment analyse gene enrichment with EGSEA test_gene_overrepresentation analyse gene over-representation with GSEA test_gene_rank analyse gene rank with GSEA test_stratification_cellularity Test of stratification of biological replicates based on tissue composition, one cell-type at the time, using Kaplan-meier curves. tidybulk Creates an annotated 'tidybulk' tibble from a 'tbl' or 'SummarizedExperiment' object tidybulk_SAM_BAM Creates a 'tt' object from a list of file names of BAM/SAM tximeta_summarizeToGene_object Needed for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximeta unnest 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