| LibraryAnnotations-class |
Man page
|
| MageckGeneRRA-class |
Man page
|
| MageckSgrnaRRA-class |
Man page
|
| SampleCounts-class |
Man page
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| SampleMetadata-class |
Man page
|
| add_bagel_classifications |
Man page
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| add_pseudocount |
Man page
Source code
|
| average_guide_bfs |
Man page
Source code
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| average_replicates |
Man page
Source code
|
| bagel_gene_infile_options |
Man page
Source code
|
| bagel_normalisation_options |
Man page
Source code
|
| bagel_normalise_counts |
Man page
Source code
|
| basic_infile_options |
Man page
Source code
|
| basic_outfile_options |
Man page
Source code
|
| calculate_gene_lfc |
Man page
Source code
|
| calculate_gini_index |
Man page
Source code
|
| calculate_lfc |
Man page
Source code
|
| calculate_lfc_options |
Man page
Source code
|
| check_dataframe |
Man page
Source code
|
| check_directory |
Man page
Source code
|
| check_file |
Man page
Source code
|
| check_is_numeric_and_is_integer |
Man page
Source code
|
| check_option |
Man page
Source code
|
| compare_annotations |
Man page
|
| compare_count_matrix_to_library |
Man page
|
| compare_counts_to_library |
Man page
|
| compare_matrix_to_sample_metadata |
Man page
|
| convert_sample_counts_objects_to_count_matrix |
Man page
Source code
|
| convert_variable_to_integer |
Man page
Source code
|
| convert_variable_to_numeric |
Man page
Source code
|
| correlation_options |
Man page
Source code
|
| count_column_index_options |
Man page
Source code
|
| count_format_options |
Man page
Source code
|
| count_library_outfile_options |
Man page
Source code
|
| count_matrix_stats |
Man page
Source code
|
| count_path_options |
Man page
Source code
|
| count_skip_options |
Man page
Source code
|
| count_type_options |
Man page
Source code
|
| counts |
Man page
|
| counts,SampleCounts-method |
Man page
|
| crisprcleanr_correction_options |
Man page
Source code
|
| crisprcleanr_normalisation_options |
Man page
Source code
|
| crisprcleanr_output_options |
Man page
Source code
|
| duplicate_guide_options |
Man page
Source code
|
| filter_by_index_options |
Man page
Source code
|
| filtered_guide_output_options |
Man page
Source code
|
| fold_change_column_index_options |
Man page
Source code
|
| fold_change_format_options |
Man page
Source code
|
| fold_change_path_options |
Man page
Source code
|
| gene_summary_top_n_genes |
Man page
Source code
|
| get_bagel_statistics |
Man page
|
| get_column_indices |
Man page
Source code
|
| get_file_class |
Man page
Source code
|
| get_guides_failing_filter |
Man page
Source code
|
| get_guides_with_no_coordinates |
Man page
Source code
|
| get_library_annotations |
Man page
|
| get_library_annotations,LibraryAnnotations-method |
Man page
|
| get_mageck_gene_summary |
Man page
|
| get_mageck_gene_summary,MageckGeneRRA-method |
Man page
|
| get_mageck_sgrna_gene_results |
Man page
|
| get_mageck_sgrna_gene_results,MageckSgrnaRRA-method |
Man page
|
| get_mageck_sgrna_summary |
Man page
|
| get_mageck_sgrna_summary,MageckSgrnaRRA-method |
Man page
|
| get_sample_metadata |
Man page
|
| get_sample_metadata,SampleMetadata-method |
Man page
|
| gini_index_per_sample |
Man page
Source code
|
| infile_column_index_options |
Man page
Source code
|
| infile_format_options |
Man page
Source code
|
| intermediate_qc_options |
Man page
Source code
|
| library_annotation_column_index_options |
Man page
Source code
|
| library_annotation_format_options |
Man page
Source code
|
| library_annotation_genomic_column_index_options |
Man page
Source code
|
| library_annotation_options |
Man page
Source code
|
| library_has_coordinates |
Man page
|
| library_has_coordinates,LibraryAnnotations-method |
Man page
|
| low_counts_per_sample |
Man page
Source code
|
| mageck_rra_summary_options |
Man page
Source code
|
| plot_common_barplot |
Man page
Source code
|
| plot_common_density_ridges |
Man page
Source code
|
| plot_common_violin |
Man page
Source code
|
| plot_correlation |
Man page
Source code
|
| plot_mageck_rra_gene_volcano |
Man page
Source code
|
| plot_mageck_rra_sgrna_barplot |
Man page
Source code
|
| plot_mapping_statistics |
Man page
Source code
|
| plot_pca |
Man page
|
| plot_roc |
Man page
Source code
|
| prepare_essentiality_data |
Man page
|
| prepare_filepath |
Man page
Source code
|
| prepare_pca |
Man page
Source code
|
| process_column_indices |
Man page
Source code
|
| process_roc |
Man page
Source code
|
| read_count_matrix_file |
Man page
Source code
|
| read_file_to_dataframe |
Man page
Source code
|
| read_fold_change_matrix_file |
Man page
Source code
|
| read_library_annotation_file |
Man page
Source code
|
| read_mageck_rra_gene_summary |
Man page
Source code
|
| read_mageck_rra_sgrna_summary |
Man page
Source code
|
| read_sample_count_file |
Man page
Source code
|
| read_sample_count_files |
Man page
Source code
|
| read_sample_metadata_file |
Man page
Source code
|
| remove_guide_options |
Man page
Source code
|
| remove_guides_from_count_matrix |
Man page
Source code
|
| remove_guides_from_library_annotations_object |
Man page
Source code
|
| remove_guides_from_sample_counts |
Man page
Source code
|
| remove_no_coordinate_guide_options |
Man page
Source code
|
| reorder_count_matrix_by_sample_type |
Man page
Source code
|
| sample_metadata_format_options |
Man page
Source code
|
| sample_metadata_options |
Man page
Source code
|
| sample_metadata_sample_filename_column_index_options |
Man page
Source code
|
| sample_metadata_sample_group_column_index_options |
Man page
Source code
|
| sample_metadata_sample_label_column_index_options |
Man page
Source code
|
| sample_metadata_sample_read_count_column_index_options |
Man page
Source code
|
| sample_metadata_sample_type_column_index_options |
Man page
Source code
|
| save_plot_list |
Man page
Source code
|
| save_plot_with_ggsave |
Man page
Source code
|
| scaling_options |
Man page
Source code
|
| sequencing_qc_options |
Man page
Source code
|
| shared_output_options |
Man page
Source code
|
| strip_id_options |
Man page
Source code
|
| total_counts_per_sample |
Man page
Source code
|
| write_dataframe_to_file |
Man page
Source code
|
| write_rdata_to_file |
Man page
Source code
|
