# Single-cell RNAseq cell cluster labelling by reference

## Documentation for package ‘celaref’ version 1.31.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

contrast_each_group_to_the_rest | contrast_each_group_to_the_rest
contrast_each_group_to_the_rest_for_norm_ma_with_limma | contrast_each_group_to_the_rest_for_norm_ma_with_limma
contrast_the_group_to_the_rest | contrast_the_group_to_the_rest
contrast_the_group_to_the_rest_with_limma_for_microarray | contrast_the_group_to_the_rest_with_limma_for_microarray
convert_se_gene_ids | convert_se_gene_ids
demo_cell_info_table | Demo cell info table
demo_counts_matrix | Demo count matrix
demo_gene_info_table | Demo gene info table
demo_microarray_expr | Demo microarray expression table
demo_microarray_sample_sheet | Demo microarray sample sheet table
demo_query_se | Demo query se (summarizedExperiment)
demo_ref_se | Demo reference se (summarizedExperiment)
de_table.demo_query | Demo query de table
de_table.demo_ref | Demo ref de table
find_within_match_differences | find_within_match_differences
get_counts_index | get_counts_index
get_inner_or_outer_ci | get_inner_or_outer_ci
get_limma_top_table_with_ci | get_limma_top_table_with_ci
get_matched_stepped_mwtest_res_table | get_matched_stepped_mwtest_res_table
get_ranking_and_test_results | get_ranking_and_test_results
get_rankstat_table | get_rankstat_table
get_reciprocal_matches | get_reciprocal_matches
get_stepped_pvals_str | get_stepped_pvals_str
get_the_up_genes_for_all_possible_groups | get_the_up_genes_for_all_possible_groups
get_the_up_genes_for_group | get_the_up_genes_for_group
get_vs_random_pval | get_vs_random_pval
load_dataset_10Xdata | load_dataset_10Xdata
load_se_from_files | load_se_from_tables
load_se_from_tables | load_se_from_tables
make_ranking_violin_plot | make_ranking_violin_plot
make_ref_similarity_names | make_ref_similarity_names
make_ref_similarity_names_for_group | make_ref_similarity_names_for_group
make_ref_similarity_names_using_marked | make_ref_similarity_names
run_pair_test_stats | run_pair_test_stats
subset_cells_by_group | subset_cells_by_group
subset_se_cells_for_group_test | subset_se_cells_for_group_test
trim_small_groups_and_low_expression_genes | trim_small_groups_and_low_expression_genes