Files in bschilder/scKirby

Automated ingestion and conversion of various single-cell data formats.

NEWS.md R/_docs.R R/activate_conda.R R/anndata_to_ctd.R R/anndata_to_list.R R/anndata_to_se.R R/anndata_to_seurat.R R/assign_cores.R R/calc_cor.R R/calc_snn.R R/calc_specificity.R R/cds_to_anndata.R R/cds_to_list.R R/cds_to_se.R R/cds_to_seurat.R R/check_annotlevels.R R/check_keys.R R/check_metadata_rownames.R R/check_se_colnames.R R/check_se_rownames.R R/check_supported.R R/check_varm.R R/converters.R R/ctd_to_se.R R/ctd_to_seurat.R R/dict_acronym.R R/dict_class.R R/dict_filetype.R R/dict_output.R R/dict_suffix.R R/dimreduc_to_list.R R/example_anndata.R R/example_list.R R/example_obj.R R/fillna_sparse.R R/get_assay_names.R R/get_cor.R R/get_n_elements.R R/get_obs.R R/get_obs_names.R R/get_obsm.R R/get_obsm_mofa.R R/get_obsp.R R/get_uns.R R/get_var.R R/get_var_names.R R/get_variable_features.R R/get_varm.R R/get_varm_mofa.R R/get_x.R R/h5seurat_to_anndata.R R/h5seurat_to_seurat.R R/has_graph.R R/hdf5_hard_save.R R/infer_graph_key.R R/ingest_data.R R/is_class.R R/is_ctd.R R/is_filetype.R R/is_installed.R R/is_list.R R/is_sparse_matrix.R R/is_suffix.R R/list_to_anndata.R R/list_to_cds.R R/list_to_dimreduc.R R/list_to_se.R R/list_to_seurat.R R/load_rdata.R R/loom_to_list.R R/loom_to_scle.R R/loom_to_se.R R/loom_to_seurat.R R/make_levels_dict.R R/map_data.R R/map_data_anndata.R R/map_data_anndata_chunked.R R/map_data_assays.R R/map_data_h5seurat.R R/map_data_matrix.R R/map_data_rowdata.R R/map_data_se.R R/map_data_seurat.R R/matrices_to_assayobjects.R R/matrix_to_se.R R/matrix_to_seurat.R R/merge_anndata.R R/merge_cds.R R/merge_sce.R R/merge_seurat.R R/messager.R R/messager_to.R R/mofa_to_dimreduc.R R/normalise.R R/package.R R/process_seurat.R R/quantize_dt.R R/quantize_matrix.R R/quantize_vector.R R/read_anndata.R R/read_data.R R/read_geo_files.R R/read_h5.R R/read_h5seurat.R R/read_loom.R R/read_matrix.R R/read_matrix_dir.R R/reimport_anndata.R R/save_anndata.R R/save_data.R R/save_h5seurat.R R/save_hdf5se.R R/sce_to_se.R R/scle_to_le.R R/se_filepath.R R/se_to_anndata.R R/se_to_le.R R/se_to_list.R R/se_to_loom.R R/se_to_sce.R R/se_to_seurat.R R/set_obs.R R/set_obsp.R R/set_uns.R R/set_var.R R/seurat1_to_list.R R/seurat_to_anndata.R R/seurat_to_cds.R R/seurat_to_h5seurat.R R/seurat_to_hdf5se.R R/seurat_to_list.R R/seurat_to_scle.R R/seurat_to_se.R R/standardise_obs.R R/stopper.R R/to_anndata.R R/to_cds.R R/to_dataframe.R R/to_datatable.R R/to_delayedarray.R R/to_graph.R R/to_list.R R/to_loom.R R/to_se.R R/to_seurat.R R/to_sparse.R R/update_seurat.R R/yeojohnson.R README.Rmd README.md inst/hex/hexSticker.Rmd man/activate_conda.Rd man/anndata_to_ctd.Rd man/anndata_to_list.Rd man/anndata_to_se.Rd man/anndata_to_seurat.Rd man/calc_cor.Rd man/cds_to_anndata.Rd man/cds_to_list.Rd man/cds_to_se.Rd man/cds_to_seurat.Rd man/class_dict.Rd man/converters.Rd man/ctd_to_se.Rd man/ctd_to_seurat.Rd man/dimreduc_to_list.Rd man/example_anndata.Rd man/example_obj.Rd man/get_cor.Rd man/get_graphs.Rd man/get_n_elements.Rd man/get_obs.Rd man/get_obs_names.Rd man/get_obsm.Rd man/get_uns.Rd man/get_var.Rd man/get_var_names.Rd man/get_variable_features.Rd man/get_varm.Rd man/get_x.Rd man/h5seurat_to_anndata.Rd man/h5seurat_to_seurat.Rd man/has_graph.Rd man/ingest_data.Rd man/is_class.Rd man/is_installed.Rd man/list_to_anndata.Rd man/list_to_dimreduc.Rd man/list_to_se.Rd man/list_to_seurat.Rd man/load_rdata.Rd man/loom_to_list.Rd man/loom_to_scle.Rd man/loom_to_se.Rd man/loom_to_seurat.Rd man/map_data.Rd man/map_data_anndata.Rd man/map_data_h5seurat.Rd man/map_data_matrix.Rd man/map_data_se.Rd man/map_data_seurat.Rd man/matrices_to_assayobjects.Rd man/matrix_to_se.Rd man/matrix_to_seurat.Rd man/merge_anndata.Rd man/merge_sce.Rd man/merge_seurat.Rd man/messager.Rd man/mofa_to_dro.Rd man/output_dict.Rd man/process_seurat.Rd man/read_data.Rd man/save_data.Rd man/scKirby-package.Rd man/sce_to_se.Rd man/scle_to_le.Rd man/se_to_anndata.Rd man/se_to_le.Rd man/se_to_list.Rd man/se_to_loom.Rd man/se_to_sce.Rd man/se_to_seurat.Rd man/set_graph.Rd man/set_obs.Rd man/set_uns.Rd man/set_var.Rd man/seurat1_to_list.Rd man/seurat_to_anndata.Rd man/seurat_to_cds.Rd man/seurat_to_h5seurat.Rd man/seurat_to_le.Rd man/seurat_to_list.Rd man/seurat_to_se.Rd man/standardise_obs.Rd man/stopper.Rd man/to_anndata.Rd man/to_delayedarray.Rd man/to_graph.Rd man/to_list.Rd man/to_loom.Rd man/to_se.Rd man/to_sparse.Rd man/update_seurat.Rd tests/testthat.R tests/testthat/test-anndata_to_ctd.R tests/testthat/test-calc_cor.R tests/testthat/test-get_cor.R tests/testthat/test-is_class.R tests/testthat/test-list_to_anndata.R tests/testthat/test-map_data.R tests/testthat/test-read_data.R tests/testthat/test-set_obsp.R tests/testthat/test-standardise_obs.R tests/testthat/test-to_graph.R tests/testthat/test-to_sparse.R vignettes/conda.Rmd vignettes/scKirby.Rmd