Files in neurogenomics/orthogene

Interspecies gene mapping

.Rbuildignore

.dockerignore

.github/.gitignore

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

.github/workflows/rworkflows.yml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/add_columns.R R/add_rowcol_names.R R/add_synonyms.R R/aggregate_mapped_genes.R R/aggregate_rows.R R/aggregate_rows_benchmark.R R/aggregate_rows_monocle3.R R/aggregate_rows_stats.R R/all_genes.R R/all_genes_babelgene.R R/all_genes_gprofiler.R R/all_genes_homologene.R R/all_ranges.R R/all_species.R R/as_delayed_array.R R/as_dict.R R/as_table.R R/check_agg_args.R R/check_agg_opts.R R/check_gene_df_type.R R/check_gene_map.R R/check_gene_output.R R/check_keep_popular.R R/check_matrix.R R/check_rownames_args.R R/check_sparseMatrix.R R/check_species_babelgene.R R/common_species_names_dict.R R/convert_orthologs.R R/create_background.R R/dMcast.R R/data.R R/drop_non121.R R/drop_nonorth_genes.R R/earthworm2human_map.R R/extract_gene_list.R R/filter_gene_df.R R/find_all_nas.R R/format_gene_df.R R/format_species.R R/gconvert_target_opts.R R/gene_input_opts.R R/gene_output_opts.R R/get_all_orgs.R R/get_data_check.R R/get_orgdb_genomeinfodbdata.R R/get_orgdb_gprofiler.R R/get_silhouettes.R R/ggtree_plot.R R/infer_species.R R/infer_species_plot.R R/invert_dictionary.R R/is_converted.R R/is_delayed_array.R R/is_human.R R/is_matrix.R R/is_sparse_matrix.R R/load_data.R R/load_rda.R R/load_rds.R R/many2many_rows.R R/map_genes.R R/map_genes_planosphere.R R/map_orthologs.R R/map_orthologs_babelgene.R R/map_orthologs_custom.R R/map_orthologs_gprofiler.R R/map_orthologs_homologene.R R/map_species.R R/map_species_check_args.R R/message_parallel.R R/messager.R R/method_fill_colors.R R/methods_opts.R R/non121_strategy_opts.R R/package.R R/plot_benchmark_bar.R R/plot_benchmark_scatter.R R/plot_orthotree.R R/plot_orthotree_metadata.R R/prepare_clades.R R/prepare_tree.R R/remove_all_nas.R R/remove_image_bg.R R/report_gene_map.R R/report_orthologs.R R/report_orthologs_i.R R/rotate_clades.R R/run_benchmark.R R/run_benchmark_once.R R/set_gprofiler.R R/sort_rows_func.R R/sparsity.R

R/sysdata.rda

R/taxa_id_dict.R R/to_sparse.R R/use_cache.R README.Rmd README.md

data/exp_mouse.rda

data/exp_mouse_enst.rda

inst/CITATION

inst/benchmark/bench_res_example.csv

inst/benchmark/benchmarks.Rmd

inst/benchmark/benchmarks.html

inst/extdata/gprofiler_namespace.csv.gz

inst/hex/hex.png

inst/hex/hexSticker.Rmd

inst/hex/hex_nowhite.png

inst/hex/purple_blue.jpeg

inst/orthogene_1.5.1.pdf man/add_synonyms.Rd man/aggregate_mapped_genes.Rd man/aggregate_rows.Rd man/aggregate_rows_monocle3.Rd man/all_genes.Rd man/all_genes_babelgene.Rd man/all_species.Rd man/check_gene_df_type.Rd man/convert_orthologs.Rd man/create_background.Rd man/dMcast.Rd man/earthworm2human_map.Rd man/exp_mouse.Rd man/exp_mouse_enst.Rd man/format_species.Rd man/get_orgdb_genomeinfodbdata.Rd man/get_silhouettes.Rd man/ggtree_plot.Rd man/gprofiler_namespace.Rd man/gprofiler_orgs.Rd man/infer_species.Rd man/infer_species_plot.Rd man/invert_dictionary.Rd man/many2many_rows.Rd man/map_genes.Rd man/map_genes_planosphere.Rd man/map_orthologs.Rd man/map_orthologs_babelgene.Rd man/map_orthologs_custom.Rd man/map_orthologs_gprofiler.Rd man/map_orthologs_homologene.Rd man/map_species.Rd man/message_parallel.Rd man/orthogene-package.Rd man/plot_benchmark_bar.Rd man/plot_benchmark_scatter.Rd man/plot_orthotree.Rd man/prepare_tree.Rd man/remove_image_bg.Rd man/report_orthologs.Rd man/run_benchmark.Rd man/set_gprofiler.Rd man/taxa_id_dict.Rd tests/testthat.R tests/testthat/test-aggregate_mapped_genes.R tests/testthat/test-all_genes.R tests/testthat/test-all_genes_babelgene.R tests/testthat/test-all_genes_gprofiler.R tests/testthat/test-all_species.R tests/testthat/test-check_rownames_args.R tests/testthat/test-convert_orthologs.R tests/testthat/test-create_background.R tests/testthat/test-earthworm2human_map.R tests/testthat/test-infer_species.R tests/testthat/test-invert_dictionary.R tests/testthat/test-load_data.R tests/testthat/test-map_genes.R tests/testthat/test-map_orthologs.R tests/testthat/test-map_orthologs_babelgene.R tests/testthat/test-map_species.R tests/testthat/test-plot_benchmark_bar.R tests/testthat/test-plot_benchmark_scatter.R tests/testthat/test-plot_orthotree.R tests/testthat/test-prepare_tree.R tests/testthat/test-report_orthologs.R tests/testthat/test-run_benchmark.R tests/testthat/test-sparsity.R tests/testthat/test-taxa_id_dict.R vignettes/docker.Rmd vignettes/infer_species.Rmd vignettes/orthogene.Rmd

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.