Files in cancerit/RCRISPR

R Functions for CRISPR-Related Analyses

NEWS.md R/ClassLibraryAnnotations.R R/ClassMageckGeneRRA.R R/ClassMageckSgrnaRRA.R R/ClassSampleCounts.R R/ClassSampleMetadata.R R/bagel_classification.R R/correlation.R R/csar_preprocessing.R R/file_helper.R R/fold_changes.R R/generic.R R/globals.R R/intermediate_qc_plots.R R/library_annotations.R R/mageck_rra.R R/normalise_counts.R R/options_helper.R R/pca.R R/raw_count_plots.R R/raw_count_statistics.R R/sample_counts.R R/sample_metadata.R README.Rmd README.md exec/BAGEL_normalisation.R exec/CRISPRcleanR_correction.R exec/CRISPRcleanR_normalisation.R exec/bagel_classification_qc.R exec/calculate_log_fold_changes.R exec/filter_by_column_indices.R exec/format_library_and_matrices_for_CRISPRcleanR.R exec/intermediate_qc.R exec/process_mageck_rra_gene_summary.R exec/raw_qc_statistics.R exec/read_sample_count_matrix.R exec/remove_duplicate_guides.R exec/remove_guides.R exec/remove_guides_without_coordinates.R exec/sample_correlations.R exec/sample_counts_to_matrix.R exec/scale_lfcs_and_bfs.R inst/extdata/external_datasets.Rmd man/LibraryAnnotations-class.Rd man/MageckGeneRRA-class.Rd man/MageckSgrnaRRA-class.Rd man/SampleCounts-class.Rd man/SampleMetadata-class.Rd man/add_bagel_classifications.Rd man/add_pseudocount.Rd man/average_guide_bfs.Rd man/average_replicates.Rd man/bagel_gene_infile_options.Rd man/bagel_normalisation_options.Rd man/bagel_normalise_counts.Rd man/basic_infile_options.Rd man/basic_outfile_options.Rd man/calculate_gene_lfc.Rd man/calculate_gini_index.Rd man/calculate_lfc.Rd man/calculate_lfc_options.Rd man/check_dataframe.Rd man/check_directory.Rd man/check_file.Rd man/check_is_numeric_and_is_integer.Rd man/check_option.Rd man/compare_annotations.Rd man/compare_count_matrix_to_library.Rd man/compare_counts_to_library.Rd man/compare_matrix_to_sample_metadata.Rd man/convert_sample_counts_objects_to_count_matrix.Rd man/convert_variable_to_integer.Rd man/convert_variable_to_numeric.Rd man/correlation_options.Rd man/count_column_index_options.Rd man/count_format_options.Rd man/count_library_outfile_options.Rd man/count_matrix_stats.Rd man/count_path_options.Rd man/count_skip_options.Rd man/count_type_options.Rd man/counts-SampleCounts-method.Rd man/counts.Rd man/crisprcleanr_correction_options.Rd man/crisprcleanr_normalisation_options.Rd man/crisprcleanr_output_options.Rd man/duplicate_guide_options.Rd man/filter_by_index_options.Rd man/filtered_guide_output_options.Rd man/fold_change_column_index_options.Rd man/fold_change_format_options.Rd man/fold_change_path_options.Rd man/gene_summary_top_n_genes.Rd man/get_bagel_statistics.Rd man/get_column_indices.Rd man/get_file_class.Rd man/get_guides_failing_filter.Rd man/get_guides_with_no_coordinates.Rd man/get_library_annotations-LibraryAnnotations-method.Rd man/get_library_annotations.Rd man/get_mageck_gene_summary-MageckGeneRRA-method.Rd man/get_mageck_gene_summary.Rd man/get_mageck_sgrna_gene_results-MageckSgrnaRRA-method.Rd man/get_mageck_sgrna_gene_results.Rd man/get_mageck_sgrna_summary-MageckSgrnaRRA-method.Rd man/get_mageck_sgrna_summary.Rd man/get_sample_metadata-SampleMetadata-method.Rd man/get_sample_metadata.Rd man/gini_index_per_sample.Rd man/infile_column_index_options.Rd man/infile_format_options.Rd man/intermediate_qc_options.Rd man/library_annotation_column_index_options.Rd man/library_annotation_format_options.Rd man/library_annotation_genomic_column_index_options.Rd man/library_annotation_options.Rd man/library_has_coordinates-LibraryAnnotations-method.Rd man/library_has_coordinates.Rd man/low_counts_per_sample.Rd man/mageck_rra_summary_options.Rd man/plot_common_barplot.Rd man/plot_common_density_ridges.Rd man/plot_common_violin.Rd man/plot_correlation.Rd man/plot_mageck_rra_gene_volcano.Rd man/plot_mageck_rra_sgrna_barplot.Rd man/plot_mapping_statistics.Rd man/plot_pca.Rd man/plot_roc.Rd man/prepare_essentiality_data.Rd man/prepare_filepath.Rd man/prepare_pca.Rd man/process_column_indices.Rd man/process_roc.Rd man/read_count_matrix_file.Rd man/read_file_to_dataframe.Rd man/read_fold_change_matrix_file.Rd man/read_library_annotation_file.Rd man/read_mageck_rra_gene_summary.Rd man/read_mageck_rra_sgrna_summary.Rd man/read_sample_count_file.Rd man/read_sample_count_files.Rd man/read_sample_metadata_file.Rd man/remove_guide_options.Rd man/remove_guides_from_count_matrix.Rd man/remove_guides_from_library_annotations_object.Rd man/remove_guides_from_sample_counts.Rd man/remove_no_coordinate_guide_options.Rd man/reorder_count_matrix_by_sample_type.Rd man/sample_metadata_format_options.Rd man/sample_metadata_options.Rd man/sample_metadata_sample_filename_column_index_options.Rd man/sample_metadata_sample_group_column_index_options.Rd man/sample_metadata_sample_label_column_index_options.Rd man/sample_metadata_sample_read_count_column_index_options.Rd man/sample_metadata_sample_type_column_index_options.Rd man/save_plot_list.Rd man/save_plot_with_ggsave.Rd man/scaling_options.Rd man/sequencing_qc_options.Rd man/shared_output_options.Rd man/strip_id_options.Rd man/total_counts_per_sample.Rd man/write_dataframe_to_file.Rd man/write_rdata_to_file.Rd tests/testthat.R tests/testthat/_snaps/bagel_classifications.md tests/testthat/_snaps/correlation.md tests/testthat/_snaps/file_helper.md tests/testthat/_snaps/fold_changes.md tests/testthat/_snaps/generic.md tests/testthat/_snaps/intermediate_qc_plots.md tests/testthat/_snaps/library_annotations.md tests/testthat/_snaps/mageck_rra.md tests/testthat/_snaps/normalise_counts.md tests/testthat/_snaps/options_helper.md tests/testthat/_snaps/pca.md tests/testthat/_snaps/raw_count_plots.md tests/testthat/_snaps/raw_count_statistics.md tests/testthat/_snaps/sample_counts.md tests/testthat/_snaps/sample_metadata.md tests/testthat/test-bagel_classifications.R tests/testthat/test-correlation.R tests/testthat/test-file_helper.R tests/testthat/test-fold_changes.R tests/testthat/test-generic.R tests/testthat/test-intermediate_qc_plots.R tests/testthat/test-library_annotations.R tests/testthat/test-mageck_rra.R tests/testthat/test-normalise_counts.R tests/testthat/test-options_helper.R tests/testthat/test-pca.R tests/testthat/test-raw_count_plots.R tests/testthat/test-raw_count_statistics.R tests/testthat/test-sample_counts.R tests/testthat/test-sample_metadata.R