Overview | Workflow | Prepare dataset | Within dataset differential expression | Query-Reference comparison | Output | Interpreting output | Assigning labels to clusters | Using the package | Installation | Quickstart | Prepare data | Input data | From tables or flat files | From 10X pipeline output | Directly with SummarizedExperiment objects | Handling large datasets | Reading microarray data | Input filtering and Pre-processing | Filtering cells and low-expression genes | Converting IDs | Within-experiment differential expression | Running comparisions | Compare groups to reference | Compare groups within a single dataset | Make labels for groups | Special case: Saving get_the_up_genes_for_all_possible_groups output | Example Analyses | PBMCs - 10X vs Microarray Reference | Prepare 10X query dataset | Prepare reference microarray dataset | Compare 10X query PBMCs to to reference | Mouse tissues - Similar and different | Load and compare mouse brain datasets | Load lacrimal gland dataset | Cross-tissue comparision | Session Info | References
Package: celaref 1.31.0
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_1.31.0.tar.gz
celaref_1.31.0.zip(r-4.7)celaref_1.31.0.zip(r-4.6)celaref_1.31.0.zip(r-4.5)
celaref_1.31.0.tgz(r-4.6-any)celaref_1.31.0.tgz(r-4.5-any)
celaref_1.31.0.tar.gz(r-4.7-any)celaref_1.31.0.tar.gz(r-4.6-any)
celaref_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
celaref/json (API)
| # Install 'celaref' in R: |
| install.packages('celaref', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- 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-1.31.0(bioc 3.24)celaref-1.30.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:3b5d808a49. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 187 | ||
| linux-devel-x86_64 | NOTE | 374 | ||
| source / vignettes | OK | 339 | ||
| linux-release-x86_64 | NOTE | 329 | ||
| macos-release-arm64 | NOTE | 169 | ||
| macos-oldrel-arm64 | NOTE | 184 | ||
| windows-devel | NOTE | 262 | ||
| windows-release | NOTE | 221 | ||
| windows-oldrel | NOTE | 251 | ||
| wasm-release | OK | 164 |
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:abindBiobaseBiocGenericsbitbit64clicliprcpp11crayondata.tableDelayedArraydplyrfarvergenericsGenomicRangesggplot2gluegtablehmsIRangesisobandlabelinglatticelifecyclemagrittrMASTMatrixMatrixGenericsmatrixStatspillarpkgconfigplyrprettyunitsprogressR6RColorBrewerRcppreadrreshape2rlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimenttibbletidyselecttzdbutf8vctrsviridisLitevroomwithrXVector
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 |
