Files in nf-osi/nfportalutils
NF Portal Utilities
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/docker.yml
.github/workflows/pkgdown.yaml
.gitignore
CODE_OF_CONDUCT.md
DESCRIPTION
Dockerfile
LICENSE
LICENSE.md
NAMESPACE
R/access_utils.R
R/add_publication_from_pubmed.R
R/add_publication_from_unpaywall.R
R/annotation_qc.R
R/annotations.R
R/assign_study_data_types.R
R/basic_utils.R
R/calculate_related_studies.R
R/cbioportal.R
R/cboilerplate.R
R/check_wiki_links.R
R/citation.R
R/convert_to_stringlist.R
R/datasets.R
R/diagrams.R
R/find.R
R/login.R
R/missing_annotations_email.R
R/new_project.R
R/nextflow_annotation_utils.R
R/nextflow_testing_utils.R
R/nextflow_utils_reports.R
R/provenance.R
R/query.R
R/register_study.R
R/remanifest.R
R/schema_utils.R
R/update_people_table.R
R/update_study_annotations.R
R/utils-pipe.R
R/view_fix.R
R/views.R
R/wiki_mod.R
R/zzz.R
README.md
_pkgdown.yml
example_script/check_wiki_links_studies.R
example_script/new_project.R
example_script/update_portal_values.R
example_script/wiki_mod_example.R
inst/rmarkdown/templates/checkpoint-closeout-report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/checkpoint-closeout-report/template.yaml
man/add_activity.Rd
man/add_activity_batch.Rd
man/add_default_fileview.Rd
man/add_default_folders.Rd
man/add_default_wiki.Rd
man/add_new_study_meta.Rd
man/add_people_from_table.Rd
man/add_publication_from_pubmed.Rd
man/add_publication_from_unpaywall.Rd
man/add_publications_from_file.Rd
man/add_study_summary.Rd
man/add_to_collection.Rd
man/add_to_scope.Rd
man/adjust_list_length.Rd
man/adjust_string_size.Rd
man/adjust_view.Rd
man/annotate_aligned_reads.Rd
man/annotate_called_variants.Rd
man/annotate_cnv.Rd
man/annotate_expression.Rd
man/annotate_reports_sarek.Rd
man/annotate_with_manifest.Rd
man/annotate_with_tool_stats.Rd
man/append_kv.Rd
man/as_coll_items.Rd
man/as_mmd_link.Rd
man/as_mmd_node.Rd
man/as_table_schema.Rd
man/assign_study_data_types.Rd
man/bad_url.Rd
man/bare_syn_id.Rd
man/bipartite_mmd_template.Rd
man/button_widget.Rd
man/byte_budget.Rd
man/calc_study_dist_dtm.Rd
man/calculate_related_studies.Rd
man/cbp_add_clinical.Rd
man/cbp_add_cna.Rd
man/cbp_add_expression.Rd
man/cbp_add_maf.Rd
man/cbp_datatypes.Rd
man/cbp_new_cancer_type.Rd
man/cbp_new_study.Rd
man/check_access.Rd
man/check_byte_budget_col_swap.Rd
man/check_cbp_study_id.Rd
man/check_readpair_validity.Rd
man/check_wiki_links.Rd
man/checked_message.Rd
man/cite_dataset.Rd
man/convert_to_stringlist.Rd
man/copy.Rd
man/copy_annotations.Rd
man/data_curator_app_subpage.Rd
man/delete_provenance.Rd
man/derive_annotations.Rd
man/dot-add_publication_from_pubmed.Rd
man/dot-check_login.Rd
man/dot-delim_string_to_vector.Rd
man/dot-modify_annotation.Rd
man/dot-replace_string_column_with_stringlist_column.Rd
man/dot-store_rows.Rd
man/dot-update_table_data.Rd
man/dot-update_view_data.Rd
man/dsp_dataset_mapping.Rd
man/dt_read.Rd
man/find_child.Rd
man/find_child_type.Rd
man/find_data_root.Rd
man/find_in.Rd
man/find_nf_asset.Rd
man/format_gene_expression_data.Rd
man/from_pubmed.Rd
man/gather_annotations.Rd
man/get_by_prop_from_json_schema.Rd
man/get_cbio_filename.Rd
man/get_dependency_from_json_schema.Rd
man/get_doi_meta.Rd
man/get_project_wiki.Rd
man/get_valid_values_from_json_schema.Rd
man/grant_specific_file_access.Rd
man/identify_read_pair.Rd
man/infer_data_type.Rd
man/is_dataset.Rd
man/is_dataset_collection.Rd
man/is_file.Rd
man/is_valid_syn_id.Rd
man/is_valid_team.Rd
man/is_valid_user.Rd
man/key_label_to_id.Rd
man/latest_version.Rd
man/list_project_datasets.Rd
man/make_admin.Rd
man/make_cbio_clinical_header.Rd
man/make_folder.Rd
man/make_meta_clinical_generic.Rd
man/make_meta_cna.Rd
man/make_meta_expression.Rd
man/make_meta_genomic_generic.Rd
man/make_meta_maf.Rd
man/make_meta_patient.Rd
man/make_meta_sample.Rd
man/make_meta_study_generic.Rd
man/make_public.Rd
man/make_public_viewable.Rd
man/manifest_generate.Rd
man/manifest_passed.Rd
man/manifest_validate.Rd
man/map_reports_sarek.Rd
man/map_sample_input_ss.Rd
man/map_sample_io.Rd
man/map_sample_output_rnaseq.Rd
man/map_sample_output_sarek.Rd
man/match_col.Rd
man/meta_qc_dataset.Rd
man/meta_qc_project.Rd
man/missing_annotation_email.Rd
man/new_col.Rd
man/new_dataset.Rd
man/new_project.Rd
man/new_project_strict.Rd
man/new_view.Rd
man/nf_cnv_dataset.Rd
man/nf_sarek_datasets.Rd
man/nf_star_salmon_datasets.Rd
man/nf_workflow_version.Rd
man/pipe.Rd
man/ppp_mmd_template.Rd
man/precheck_manifest.Rd
man/processing_flowchart.Rd
man/register_study.Rd
man/register_study_files.Rd
man/remanifest.Rd
man/remove_button.Rd
man/remove_wiki_subpage.Rd
man/save_manifest.Rd
man/schema_max_str_len.Rd
man/strlist_JSON.Rd
man/summarize_attribute.Rd
man/summarize_file_access.Rd
man/swap_col.Rd
man/syn_login.Rd
man/table_query.Rd
man/tersely.Rd
man/test_failed.Rd
man/test_passed.Rd
man/update_items.Rd
man/update_study_annotations.Rd
man/use_latest_in_collection.Rd
man/use_ref_map.Rd
man/walk.Rd
man/which_coll_type.Rd
man/wiki_mod.Rd
man/write_cbio_clinical.Rd
man/write_meta.Rd
nfportalutils.Rproj
tests/README.md
tests/testthat.R
tests/testthat/helpers.R
tests/testthat/setup_mock_data.R
tests/testthat/test-add_pubmed_publications.R
tests/testthat/test_auth_login.R
tests/testthat/test_collection_utils.R
tests/testthat/test_dataset_utils.R
tests/testthat/test_json_schema_utils.R
tests/testthat/test_new_project_strict.R
tests/testthat/test_register_study.R
tests/testthat/test_synapse_schema_utils.R
vignettes/.gitignore
vignettes/annotate-nf-processed-data.Rmd
vignettes/bringing-portal-data-to-other-platforms-cbioportal.Rmd
vignettes/manifest_rd1.csv
vignettes/revalidation-workflows.Rmd
vignettes/revalidation-workflows.Rmd.orig
vignettes/survey-public-files.Rmd
