Man pages for stemangiola/ttSc
Friendly tidy wrappers for facilitating transcriptional analyses
| add_adjusted_counts_for_unwanted_variation_sc | Add addjust counts for unwanted variation |
| add_assay | Add assay to a seurat object |
| add_attr | Add attribute to abject |
| add_cell_cycle_annotation_sc | Add cell cyle annotation |
| add_cell_type_annotation_sc | Add cell type information on single cells |
| add_class | Add class to abject |
| add_cluster_annotation_SNN_sc | Add cluster information of single cells |
| add_doublet_classification_sc | Add doublet classification |
| add_mitochndrion_transcription_abundance_sc | Add mitochondrion transcription abundance |
| add_normalised_counts_sc | Add normalised counts |
| add_reduced_dimensions_PCA | Add principal .dims |
| add_reduced_dimensions_TSNE | Add TSNE dimensions |
| add_reduced_dimensions_UMAP | Add UMAP dimensions |
| add_rotated_dimensions_sc | Add Rotated dimensions of two principal .dims or MDS... |
| add_variable_genes_classification | Add variable gene annotation |
| adjust_abundance | Adjust transcript abundance for unwanted variation |
| aggregate_cells-methods | Creates a 'tt' object |
| aggregate_cells-Seurat-method | aggregate_cells |
| aggregate_cells-SingleCellExperiment-method | aggregate_cells |
| aggregate_duplicated_transcripts_sc | Aggregates multiple counts from the same samples/cells (e.g.,... |
| aggregate_duplicated_transcripts_wide_sc | Aggregates multiple counts from the same samples/cells in a... |
| aggregate_duplicates | Aggregates multiple counts from the same samples (e.g., from... |
| annotate_symbol | Add transcript symbol column from ensembl id |
| as_matrix | Get matrix from tibble |
| cluster_elements | Get clusters of elements (e.g., samples or transcripts) |
| create_seurat_from_tibble | Create seurat object from tibble |
| create_seurat_from_tibble_wide | Create seurat object from tibble |
| create_tt_from_cellRanger_sc | Create tt object from cellRanger results |
| create_tt_from_seurat | Create tt object from seurat object |
| create_tt_from_tibble_sc | Create tt object from tibble |
| create_tt_from_tibble_wide_sc | Create tt object from tibble |
| deconvolve_cellularity | Get cell type proportions from samples |
| do_integration_seurat | Integrate many seurat objects |
| drop_assay | Drop assay of a seurat object |
| drop_attr | Drop attribute to abject |
| drop_class | Remove class to abject |
| error_if_counts_is_na | Check whether there are NA counts |
| error_if_duplicated_genes | Check whether there are duplicated genes/transcripts |
| error_if_log_transformed | Check whether a numeric vector has been log transformed |
| error_if_wrong_input | Check whether there are NA counts |
| extract_abundance | Add differential transcription information to a tbl using... |
| get_abundance_sc_long | get abundance long |
| get_abundance_sc_wide | get abundance long |
| get_adjusted_counts_for_unwanted_variation_sc | Get adjusted counts for unwanted variation |
| get_cell | Get column names either from user or from attributes |
| get_cell_cycle_annotation_sc | Get cell cyle annotation |
| get_cell_type_annotation_sc | Get cell type information on single cells |
| get_cluster_annotation_SNN_automatic | Get cluster information of single cells |
| get_cluster_annotation_SNN_sc | Get cluster information of single cells |
| get_mitochndrion_transcription_abundance_sc | Calculate mitochondrion transcription abundance |
| get_normalised_counts_sc | Get normalised counts |
| get_reduced_dimensions_PCA | Get principal .dims |
| get_reduced_dimensions_TSNE | Get TSNE dimensions |
| get_reduced_dimensions_UMAP | Get UMAP dimensions |
| get_rotated_dimensions_sc | Get rotated dimensions of two principal .dims or MDS... |
| hello | Hello, World! |
| ifelse2_pipe | This is a generalisation of ifelse that acceots an object and... |
| ifelse3_pipe | This is a generalisation of ifelse that acceots an object and... |
| ifelse_pipe | This is a generalisation of ifelse that acceots an object and... |
| iterate_cell_cycle_scoreing | Add variable gene annotation This function is needed for a... |
| merged_tt_object | Add cell type information on single cells |
| parse_formula | Formula parser |
| prepend | From rlang deprecated |
| reduce_dimensions | Dimension reduction of the transcript abundance data |
| remove_redundancy | Drop redundant elements (e.g., samples) for which feature... |
| rename_sample_if_samples_not_set_by_user | Check if sample already set by the user, otherwise take... |
| rotate_dimensions | Rotate two dimensions (e.g., principal .dims) of an arbitrary... |
| scale_abundance | Normalise the counts of transcripts/genes |
| scale_design | Scale design matrix |
| select_closest_pairs | Sub function of... |
| set_default_assay_seurat | Set defauly assay of a seurat object |
| test_differential_abundance | Add differential transcription information to a tbl using... |
| tidysc | Creates a 'tt' object from a 'tbl" |
| tidysc_cell_ranger.default | #' @export tidysc_cell_ranger.default <- function(dir_names,... |
| update_object_sc | Update seurat attribute based on cell content of the data tt... |
