Package: celaref 1.25.0
Sarah Williams
celaref: Single-cell RNAseq cell cluster labelling by reference
After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).
Authors:
celaref_1.25.0.tar.gz
celaref_1.25.0.zip(r-4.5)celaref_1.25.0.zip(r-4.4)celaref_1.25.0.zip(r-4.3)
celaref_1.25.0.tgz(r-4.4-any)celaref_1.25.0.tgz(r-4.3-any)
celaref_1.25.0.tar.gz(r-4.5-noble)celaref_1.25.0.tar.gz(r-4.4-noble)
celaref_1.25.0.tgz(r-4.4-emscripten)celaref_1.25.0.tgz(r-4.3-emscripten)
celaref.pdf |celaref.html✨
celaref/json (API)
NEWS
| # Install 'celaref' in R: |
| install.packages('celaref', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- de_table.demo_query - Demo query de table
- de_table.demo_ref - Demo ref de table
- 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
- demo_ref_se - Demo reference se
On BioConductor:celaref-1.25.0(bioc 3.21)celaref-1.24.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:34ca877c5c. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:contrast_each_group_to_the_restcontrast_each_group_to_the_rest_for_norm_ma_with_limmaconvert_se_gene_idsget_rankstat_tableget_the_up_genes_for_all_possible_groupsget_the_up_genes_for_groupload_dataset_10Xdataload_se_from_filesload_se_from_tablesmake_ranking_violin_plotmake_ref_similarity_namesmake_ref_similarity_names_using_markedsubset_cells_by_grouptrim_small_groups_and_low_expression_genes
Dependencies:abindaskpassBiobaseBiocGenericsbitbit64clicliprcolorspacecpp11crayoncurldata.tableDelayedArraydplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehmshttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMASTMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrprettyunitsprogressR6RColorBrewerRcppreadrreshape2rlangS4ArraysS4VectorsscalesSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 query de table | de_table.demo_query |
| Demo ref de table | de_table.demo_ref |
| Demo cell info table | demo_cell_info_table |
| Demo count matrix | demo_counts_matrix |
| Demo gene info table | demo_gene_info_table |
| Demo microarray expression table | demo_microarray_expr |
| Demo microarray sample sheet table | demo_microarray_sample_sheet |
| Demo query se (summarizedExperiment) | demo_query_se |
| Demo reference se (summarizedExperiment) | demo_ref_se |
| 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_tables | load_se_from_files load_se_from_tables |
| make_ranking_violin_plot | make_ranking_violin_plot |
| make_ref_similarity_names | make_ref_similarity_names make_ref_similarity_names_using_marked |
| make_ref_similarity_names_for_group | make_ref_similarity_names_for_group |
| 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 |
