Files in NathanSkene/MAGMA_Celltyping
Find Causal Cell-Types Underlying Complex Trait Genetics

.DS_Store

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/rworkflows.yml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/adjust_zstat_in_genesOut.r R/as_package_version.R R/ask_integer.R R/build_snp_location_tables.r R/calculate_celltype_associations.r R/calculate_celltype_associations_linear.R R/calculate_celltype_associations_top10.R R/calculate_celltype_enrichment_limma.r R/calculate_conditional_celltype_associations.R R/calculate_conditional_celltype_enrichment_limma.R R/calculate_conditional_geneset_enrichment.R R/calculate_geneset_enrichment.r R/capture.R R/celltype_associations_pipeline.r R/check_access.R R/check_analysis_name.R R/check_controlledCTs.R R/check_controlled_celltypes.R R/check_duplicate.R R/check_enrichment_mode.R R/check_entrez_genes.R R/check_genomeLocFile.R R/check_inputs_to_magma_celltype_analysis.r R/check_n.R R/check_quantiles.R R/check_synonym_dup.R R/compare_trait_enrichment.r R/copy_snps_to_genes_files.R R/create_DT.R R/create_fake_gwas_path.R R/create_gene_covar_file.r R/create_gene_covar_file_mode.R R/create_genesets.R R/create_top10percent_genesets_file.R R/data.r R/decompress.R R/drop_genes_within_mhc.r R/filter_by_orthologs.r R/find_GenesOut_files.R R/find_install_dir.R R/fix_celltype_names2.R R/fix_path.R R/format_sumstats_for_magma.r R/format_sumstats_for_magma_macOnly.R R/get_actual_path.R R/get_ctd.R R/get_ctd_dendro.r R/get_data.R R/get_data_check.R R/get_deciles_matrix.R R/get_driver_genes.R R/get_example_gwas.R R/get_example_gwas_raw.R R/get_example_magma_files.R R/get_gene_info.R R/get_genomeLocFile.R R/get_genome_ref.R R/get_genome_ref_magma.R R/get_genome_ref_piggyback.R R/get_genomebuild_for_sumstats.r R/get_magma_paths.r R/get_os.R R/get_sub_SNP_LOC_DATA.R R/github_download_files.R R/github_list_files.R R/import_magma_files.r R/import_magma_files_metadata.R R/import_magma_files_renest.R R/import_magma_files_sort.R R/import_magma_files_tables.R R/infer_ctd_species.R R/infer_geneset_species.R R/invert_dict.R R/is_32bit.R R/iterate_conditional_celltypes.R R/iterate_conditional_celltypes_grouped.R R/list_remote_files.R R/list_snps2genes_files.R R/load_magma_results_file.r R/load_rdata.R R/load_snp_loc_data.r R/magma_check.R R/magma_check_version_match.R R/magma_download_binary.R R/magma_executable.R R/magma_executable_select.R R/magma_find_executable.R R/magma_install.R R/magma_installed.R R/magma_installed_version.R R/magma_links.R R/magma_links_gather.R R/magma_links_query.R R/magma_links_versions.R R/magma_os_suffix.R R/magma_read_covar_out.R R/magma_read_sets_out.R R/magma_run.R R/magma_tileplot.r R/magma_uninstall.R R/map_snps_to_genes.r R/map_specificity_to_entrez.r R/merge_magma_results.r R/merge_results.R R/message_cmd.R R/message_parallel.r R/messager.R R/mungesumstats_deprecation_msg.R R/plot_celltype_associations.r R/prepare_quantile_groups.r R/read_magma_genes_out.R R/read_magma_genes_raw.R R/results_heatmap.R R/set_permissions.R R/standardise.sumstats.column.headers.R R/standardise.sumstats.column.headers.crossplatform.R R/startup_msg.R R/stopper.R R/zzz.R README.Rmd README.md

data/enrichment_results.rda

data/gwas_munged.rda

data/hgnc2entrez_orthogene.rda

data/magma_files_metadata.rda

data/magma_links_stored.rda

data/rbfox_binding.rda

inst/CITATION

inst/extdata/MAGMA_Celltyping_1.0_vignette.R

inst/extdata/MAGMA_Files/ieu-a-298/ieu-a-298.genes.out

inst/extdata/MAGMA_Files/ieu-a-298/ieu-a-298.genes.raw

inst/extdata/Magma_Column_headers.csv

inst/extdata/ieu-a-298.tsv.gz.35UP.10DOWN.level1.MainRun.gsa.out

inst/hex/hex.png

inst/hex/hexSticker.Rmd

inst/hex/volcano_black.png

NathanSkene/MAGMA_Celltyping documentation built on Aug. 21, 2023, 8:55 a.m.

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NathanSkene/MAGMA_Celltyping
Find Causal Cell-Types Underlying Complex Trait Genetics

Files in NathanSkene/MAGMA_Celltyping
Find Causal Cell-Types Underlying Complex Trait Genetics

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NathanSkene/MAGMA_Celltyping Find Causal Cell-Types Underlying Complex Trait Genetics

Files in NathanSkene/MAGMA_Celltyping Find Causal Cell-Types Underlying Complex Trait Genetics

R Package Documentation

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We want your feedback!

NathanSkene/MAGMA_Celltyping
Find Causal Cell-Types Underlying Complex Trait Genetics

Files in NathanSkene/MAGMA_Celltyping
Find Causal Cell-Types Underlying Complex Trait Genetics