Files in MonashBioinformaticsPlatform/celaref
Single-cell RNAseq cell cluster labelling by reference
.Rbuildignore
.github/README.html
.github/README.md
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/contrasting_functions.r
R/data.r
R/group_labelling_functions.r
R/loading_helper_functions.r
R/plotting_functions.R
data/de_table.demo_query.rda
data/de_table.demo_ref.rda
data/demo_cell_info_table.rda
data/demo_counts_matrix.rda
data/demo_gene_info_table.rda
data/demo_microarray_expr.rda
data/demo_microarray_sample_sheet.rda
data/demo_query_se.rda
data/demo_ref_se.rda
inst/extdata/demo_microarray_expression.tab
inst/extdata/demo_microarray_info.tab
inst/extdata/larger_doco_examples.rdata
inst/extdata/sim_cr_dataset/analysis/clustering/kmeans_4_clusters/clusters.csv
inst/extdata/sim_cr_dataset/filtered_gene_bc_matrices/GRCh38/barcodes.tsv
inst/extdata/sim_cr_dataset/filtered_gene_bc_matrices/GRCh38/genes.tsv
inst/extdata/sim_cr_dataset/filtered_gene_bc_matrices/GRCh38/matrix.mtx
inst/extdata/sim_query_cell_info.tab
inst/extdata/sim_query_counts.tab
inst/extdata/sim_query_gene_info.tab
inst/extdata/sim_ref_cell_info.tab
inst/extdata/sim_ref_counts.tab
inst/extdata/sim_ref_gene_info.tab
man/contrast_each_group_to_the_rest.Rd
man/contrast_each_group_to_the_rest_for_norm_ma_with_limma.Rd
man/contrast_the_group_to_the_rest.Rd
man/contrast_the_group_to_the_rest_with_limma_for_microarray.Rd
man/convert_se_gene_ids.Rd
man/de_table.demo_query.Rd
man/de_table.demo_ref.Rd
man/demo_cell_info_table.Rd
man/demo_counts_matrix.Rd
man/demo_gene_info_table.Rd
man/demo_microarray_expr.Rd
man/demo_microarray_sample_sheet.Rd
man/demo_query_se.Rd
man/demo_ref_se.Rd
man/find_within_match_differences.Rd
man/get_counts_index.Rd
man/get_inner_or_outer_ci.Rd
man/get_limma_top_table_with_ci.Rd
man/get_matched_stepped_mwtest_res_table.Rd
man/get_ranking_and_test_results.Rd
man/get_rankstat_table.Rd
man/get_reciprocal_matches.Rd
man/get_stepped_pvals_str.Rd
man/get_the_up_genes_for_all_possible_groups.Rd
man/get_the_up_genes_for_group.Rd
man/get_vs_random_pval.Rd
man/load_dataset_10Xdata.Rd
man/load_se_from_tables.Rd
man/make_ranking_violin_plot.Rd
man/make_ref_similarity_names.Rd
man/make_ref_similarity_names_for_group.Rd
man/run_pair_test_stats.Rd
man/subset_cells_by_group.Rd
man/subset_se_cells_for_group_test.Rd
man/trim_small_groups_and_low_expression_genes.Rd
tests/testthat.R
tests/testthat/test-contrasting_functions.R
tests/testthat/test-loading_helper_functions.R
vignettes/celaref.bib
vignettes/celaref_doco.Rmd
vignettes/images/pbmc4k_cloupe_kmeans7.png
vignettes/images/violin_plot_example.png
vignettes/images/workflow_diagram.png
