Man pages for stemangiola/tidyBulk
Brings transcriptomics to the tidyverse
| adjust_abundance-methods | Adjust transcript abundance for unwanted variation |
| aggregate_duplicates-methods | Aggregates multiple counts from the same samples (e.g., from... |
| arrange-methods | Arrange rows by column values |
| as_matrix | Get matrix from tibble |
| as_SummarizedExperiment-methods | as_SummarizedExperiment |
| bind_rows | Efficiently bind multiple data frames by row and column |
| breast_tcga_mini_SE | Needed for vignette breast_tcga_mini_SE |
| check_if_counts_is_na | Check whether there are NA counts |
| check_if_duplicated_genes | Check whether there are duplicated genes/transcripts |
| check_if_wrong_input | Check whether there are NA counts |
| cluster_elements-methods | Get clusters of elements (e.g., samples or transcripts) |
| counts_ensembl | Counts with ensembl annotation |
| deconvolve_cellularity-methods | Get cell type proportions from samples |
| describe_transcript-methods | Get DESCRIPTION from gene SYMBOL for Human and Mouse |
| distinct-methods | distinct |
| dplyr-methods | Left join datasets |
| ensembl_symbol_mapping | Data set |
| ensembl_to_symbol-methods | Add transcript symbol column from ensembl id for human and... |
| fill_missing_abundance-methods | Fill transcript abundance if missing from sample-transcript... |
| filter-methods | Subset rows using column values |
| flybaseIDs | flybaseIDs |
| get_bibliography-methods | Produces the bibliography list of your workflow |
| get_reduced_dimensions_UMAP_bulk | Get UMAP |
| get_reduced_dimensions_UMAP_bulk_SE | Get UMAP |
| group_by-methods | Group by one or more variables |
| identify_abundant-methods | find abundant transcripts |
| impute_missing_abundance-methods | impute transcript abundance if missing from sample-transcript... |
| join-methods | Inner join datasets |
| keep_abundant-methods | Keep abundant transcripts |
| keep_variable-methods | Keep variable transcripts |
| log10_reverse_trans | log10_reverse_trans |
| logit_trans | logit scale |
| mutate-methods | Create, modify, and delete columns |
| nest-methods | unnest |
| pipe | Pipe operator |
| pivot_sample-methods | Extract sample-wise information |
| pivot_transcript-methods | Extract transcript-wise information |
| quantile_normalise_abundance-methods | Normalise by quantiles the counts of transcripts/genes |
| reduce_dimensions-methods | Dimension reduction of the transcript abundance data |
| reexports | Objects exported from other packages |
| remove_redundancy-methods | Drop redundant elements (e.g., samples) for which feature... |
| rename-methods | Rename columns |
| resolve_complete_confounders_of_non_interest | Resolve Complete Confounders of Non-Interest |
| resolve_complete_confounders_of_non_interest-methods | resolve_complete_confounders_of_non_interest |
| rotate_dimensions-methods | Rotate two dimensions (e.g., principal components) of an... |
| rowwise-methods | Group input by rows |
| scale_abundance-methods | Scale the counts of transcripts/genes |
| se | SummarizedExperiment |
| se_mini | SummarizedExperiment mini for vignette |
| summarise-methods | Summarise each group to fewer rows |
| symbol_to_entrez | Get ENTREZ id from gene SYMBOL |
| test_differential_abundance-methods | Perform differential transcription testing using edgeR... |
| test_differential_cellularity-methods | Add differential tissue composition information to a tbl |
| test_gene_enrichment-methods | analyse gene enrichment with EGSEA |
| test_gene_overrepresentation-methods | analyse gene over-representation with GSEA |
| test_gene_rank-methods | analyse gene rank with GSEA |
| test_stratification_cellularity-methods | Test of stratification of biological replicates based on... |
| tidybulk-methods | Creates an annotated 'tidybulk' tibble from a 'tbl' or... |
| tidybulk_SAM_BAM-methods | Creates a 'tt' object from a list of file names of BAM/SAM |
| tximeta_summarizeToGene_object | Needed for tests tximeta_summarizeToGene_object, It is... |
| 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 |
