API for NathanSkene/MAGMA_Celltyping
Find Causal Cell-Types Underlying Complex Trait Genetics
| Global functions | |
|---|---|
| .onLoad | Source code |
| adjust.zstat.in.genesOut | Source code |
| adjust_zstat_in_genesOut | Man page Source code |
| as_package_version | Source code |
| ask_integer | Source code |
| build_snp_location_tables | Man page Source code |
| calculate.celltype.enrichment.probabilities.wtLimma | Source code |
| calculate.conditional.celltype.enrichment.probabilities.wtLimma | Source code |
| calculate_celltype_associations | Man page Source code |
| calculate_celltype_associations_linear | Source code |
| calculate_celltype_associations_top10 | Source code |
| calculate_celltype_enrichment_limma | Man page Source code |
| calculate_conditional_celltype_associations | Man page Source code |
| calculate_conditional_celltype_enrichment_limma | Man page Source code |
| calculate_conditional_geneset_enrichment | Man page Source code |
| calculate_geneset_enrichment | Man page Source code |
| capture | Man page Source code |
| celltype_associations_pipeline | Man page Source code |
| check_access | Man page Source code |
| check_analysis_name | Source code |
| check_controlledCTs | Man page Source code |
| check_controlled_celltypes | Source code |
| check_duplicate | Source code |
| check_enrichment_mode | Man page Source code |
| check_entrez_genes | Man page Source code |
| check_genomeLocFile | Source code |
| check_inputs_to_magma_celltype_analysis | Man page Source code |
| check_n | Source code |
| check_quantiles | Man page Source code |
| check_synonym_dup | Source code |
| compare.trait.enrichments | Source code |
| compare_trait_enrichments | Man page Source code |
| copy_snps_to_genes_files | Man page Source code |
| create_DT | Man page Source code |
| create_fake_gwas_path | Man page Source code |
| create_gene_covar_file | Man page Source code |
| create_gene_covar_file_mode | Man page Source code |
| create_genesets | Man page Source code |
| create_top10percent_genesets_file | Man page Source code |
| decompress | Man page Source code |
| drop.genes.within.mhc | Source code |
| drop_genes_within_mhc | Man page Source code |
| enrichment_results | Man page |
| filter.by.orthologs | Source code |
| filter_by_orthologs | Man page |
| find_GenesOut_files | Man page Source code |
| find_install_dir | Man page Source code |
| fix_celltype_names2 | Man page Source code |
| fix_path | Man page Source code |
| format_sumstats_for_magma | Man page Source code |
| format_sumstats_for_magma_macOnly | Man page Source code |
| get.ctd.dendro | Source code |
| get.magma.paths | Source code |
| get_actual_path | Man page Source code |
| get_ctd | Man page Source code |
| get_ctd_dendro | Man page Source code |
| get_data | Man page Source code |
| get_data_check | Source code |
| get_deciles_matrix | Man page Source code |
| get_driver_genes | Man page Source code |
| get_example_gwas | Man page Source code |
| get_example_gwas_raw | Man page Source code |
| get_example_magma_files | Man page Source code |
| get_gene_info | Man page Source code |
| get_genomeLocFile | Man page Source code |
| get_genome_ref | Man page Source code |
| get_genome_ref_magma | Man page Source code |
| get_genome_ref_piggyback | Man page Source code |
| get_genomebuild_for_sumstats | Man page Source code |
| get_magma_paths | Man page Source code |
| get_os | Man page Source code |
| get_sub_SNP_LOC_DATA | Man page Source code |
| github_download_files | Man page Source code |
| github_list_files | Man page Source code |
| gwas_munged | Man page |
| hgnc2entrez_orthogene | Man page |
| import_magma_files | Man page Source code |
| import_magma_files_metadata | Man page Source code |
| import_magma_files_renest | Source code |
| import_magma_files_sort | Source code |
| import_magma_files_tables | Man page Source code |
| infer_ctd_species | Man page Source code |
| infer_geneset_species | Man page Source code |
| invert_dict | Man page Source code |
| is_32bit | Man page Source code |
| iterate_conditional_celltypes | Man page Source code |
| iterate_conditional_celltypes_grouped | Man page Source code |
| list_remote_files | Man page Source code |
| list_snps_to_genes_files | Man page Source code |
| load.magma.results.file | Source code |
| load_magma_results_file | Man page Source code |
| load_rdata | Man page Source code |
| load_snp_loc_data | Man page Source code |
| magma.tileplot | Source code |
| magma_check | Man page Source code |
| magma_check_version_match | Man page Source code |
| magma_download_binary | Man page Source code |
| magma_executable | Man page Source code |
| magma_executable_select | Man page Source code |
| magma_files_metadata | Man page |
| magma_find_executable | Man page Source code |
| magma_install | Man page Source code |
| magma_installed | Man page Source code |
| magma_installed_version | Man page Source code |
| magma_links | Man page Source code |
| magma_links_gather | Man page Source code |
| magma_links_query | Man page Source code |
| magma_links_stored | Man page |
| magma_links_versions | Man page Source code |
| magma_os_suffix | Man page Source code |
| magma_read_covar_out | Man page Source code |
| magma_read_sets_out | Man page Source code |
| magma_run | Man page Source code |
| magma_tileplot | Man page Source code |
| magma_uninstall | Man page Source code |
| map.snps.to.genes | Source code |
| map_snps_to_genes | Man page Source code |
| map_specificity_to_entrez | Man page Source code |
| merge_magma_results | Man page Source code |
| merge_results | Man page Source code |
| message_cmd | Source code |
| message_parallel | Man page Source code |
| messager | Man page Source code |
| mungesumstats_deprecation_msg | Man page Source code |
| plot_celltype_associations | Man page Source code |
| prepare_quantile_groups | Man page Source code |
| rbfox_binding | Man page |
| read_magma_genes_out | Man page Source code |
| read_magma_genes_raw | Man page Source code |
| results_heatmap | Man page Source code |
| set_permissions | Man page Source code |
| standardise.sumstats.column.headers | Man page Source code |
| standardise.sumstats.column.headers.crossplatform | Man page Source code |
| startup_msg | Source code |
| stopper | Source code |
