IGS/gEAR-v0.9.0.zip
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IGS-gEAR-b8995be
LICENSE
34.5 kB
README.md
2.6 kB
annotations
.gitignore
14 Bytes
bin
FACS_RNAseq_Data.loader.py
5.6 kB
add_analysis_tSNE_to_h5ad.py
2.6 kB
add_datasets_to_group.py
5.8 kB
add_ensembl_id_to_h5ad_missing_release.py
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add_ensembl_ids_to_h5ad.py
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add_ensembl_ids_to_tab_file.py
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add_gene_symbol_to_file.py
2.1 kB
add_primary_analyses_to_datasets.py
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add_projection_pattern_json.py
5.4 kB
calculate_averages_stddev.py
3.5 kB
change_gene_column_case.py
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change_ownership.py
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check_h5ad_for_missing_gene_symbol.py
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check_singlecell_column_count.py
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convert_excel_metadata_to_json.py
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convert_legacy_dataset_to_3tab.py
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convert_legacy_dataset_to_h5ad.py
1.2 kB
copy_svg_group_ids_to_class_names.py
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copy_svg_ids_to_class_names.py
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create_MEX_from_gear_standard_tab.py
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create_excel_from_gear_standard_tab.py
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export_dataset_sql.sh
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fetch_komp_repository_data.py
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find_best_ensembl_release_from_h5ad.py
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find_best_ensembl_release_match.py
2.9 kB
find_duplicated_dataset_genes.py
1.2 kB
fix_array_x_axis.py
1.2 kB
fix_double_encoded_json.py
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fix_missing_display_config_options.py
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fix_x.py
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generate_color_gradient_css.py
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generate_help_ids.py
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generate_initial_composition_plots.py
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generate_profile_share_ids.py
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generate_share_ids.data
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generate_share_ids.py
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generate_static_layouts.py
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get_email_list.py
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get_shield_pages.py
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get_site_stats.py
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h5ad_add_colors_column.py
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h5ad_convert_from_3tab.py
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h5ad_convert_from_MEX.py
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h5ad_convert_from_gear_standard_tab.py
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h5ad_convert_to_3tab.py
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h5ad_duplicate_column.py
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h5ad_fix_numeric_headers.py
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h5ad_rename_obs_column.py
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h5ad_rename_obs_index.py
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h5ad_replace_column_value.py
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h5ad_test_read.py
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komp_repository_data.p
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list_datasets.py
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load_ensembl_gbk_annotations.py
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load_genbank_annotations.py
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load_genbank_gbk_annotations.py
13.2 kB
load_gene_ontology.py
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load_gene_synonyms.py
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load_komp_repository_data.py
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load_mgi_mirna_aliases.py
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load_mirna_fam_data.py
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load_zfin_id_urls.py
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nullify_na_columns.py
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parse_apache_error_logs.py
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parse_genbank_annotations.py
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process_shield_pages.out
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process_shield_pages.py
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process_shield_pages.update.sql
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query_geo.py
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remove_marked_datasets.py
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rename_single_cell_dataset_headers.py
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replace_anatomy_ids_with_class_names.py
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report_dataset_dimensions.py
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report_dataset_usage_stats.py
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rescore_dataset_coloring_v3.py
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rescore_dataset_scope_dataset_coloring.py
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rescore_gene_scope_dataset_coloring.py
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rescore_tissue_scope_dataset_coloring.py
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set_svg_class_names.py
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shield_urls_update.sql
1.2 MB
tab_file_info.py
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test_database_connection.py
459 Bytes
test_mysql_stringtype.py
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update_dataset_long_description.py
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update_dataset_table_schematic_images.py
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update_gene_coordinates_from_genbank.py
3.7 kB
update_plotly_json_db.py
2.1 kB
validate_3tab_xls_gene_symbols.py
2.6 kB
validate_file_extension.py
2.9 kB
validate_tab_file.py
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create_schema.sql
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docker
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.gitignore
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000-default.conf
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Dockerfile
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apache2.conf
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docker-compose.yml
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docker_notes.md
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gear.ini.docker
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mysql_setup_notes.md
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php.ini
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requirements.txt
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umgear.conf
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wsgi.conf
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wsgi.load
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docs
adding_new_display_types.md
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analysis_directory_structure_conventions.txt
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cron_config.md
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ensembl.doc
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epiviz-tracks.json
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epiviz_notes-old.md
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gear_overview.png
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gear_scoring_levels.png
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h5ad_analysis_usage_convention.txt
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how_analyses_panels_are_displayed.md
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links.out
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mysql_config.md
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plugins.md
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posters
20160220_ARO_2016.pptx
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20171101_Genome_informatics.pptx
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20180705_GRC_poster.pdf
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20180705_GRC_poster.pptx
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20190211_ARO_2019.pdf
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20190211_ARO_2019.pptx
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release_test_plan.md
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setup.apache.md
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setup.epiviz.md
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setup.mysql.md
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setup.new_server.notes.md
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setup.python.md
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svg_formatting.md
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uploader_output_h5ad_format.docx
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gear.ini
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gene_ontology_ext.obo
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go.obo
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lib
__init__.py
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gear
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dataarchive.py
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datasetstats.py
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datasetuploader.py
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db.py
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email.py
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exceluploader.py
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fromgeo.py
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metadata.py
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metadatavalidator.py
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mexuploader.py
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plot.py
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plotting.py
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plotting_deprecated.py
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queue.py
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threetabuploader.py
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geardb.py
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gearqueue.py
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loaderutils.py
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notebooks
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ProjectR_development.ipynb
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dataset_read_issues.ipynb
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playground.ipynb
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primary_analysis_steps.ipynb
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seurat_analysis_path.ipynb
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tsne_subplots.ipynb
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scripts_extra
clean_dataset.py
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tests
1_absent_exp_sheet.xlsx
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2_absent_obs_sheet.xlsx
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3_obs_count_mismatch_exp.xlsx
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4_obs_name_mismatch_exp.xlsx
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5_genes_count_mismatch_exp.xlsx
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6_genes_name_mismatch_exp.xlsx
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7_exp_contains_string.xlsx
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8_exp_contains_empty_cells.xlsx
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9_absent_genes_sheet.xlsx
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base_template.xlsx
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dataset_metadata_test.xlsx
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test_case_descriptions.txt
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test_metadata_v2.xlsx
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test_metadata_v3.xlsx
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www
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by_dataset
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.htaccess
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by_user
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analyze_dataset.html
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api
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api.py
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api.wsgi
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requirements.txt
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resources
analyses.py
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available_display_types.py
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dataset_display.py
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epiviz_data.py
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gene_symbols.py
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h5ad.py
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plotly_data.py
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svg_data.py
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top_pca_genes.py
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tsne_data.py
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apple-touch-icon-precomposed.png
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delete_dataset_display.cgi
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get_dataset_info.cgi
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get_default_display.cgi
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get_index_info.cgi
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get_organism_list.cgi
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get_pattern_element_list.cgi
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get_stored_analysis.cgi
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get_stored_analysis_list.cgi
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get_user_gene_carts.cgi
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get_users_layout_members.cgi
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h5ad_apply_primary_filter.cgi
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h5ad_compare_genes.cgi
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h5ad_find_marker_genes.cgi
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test_sniffer.py
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by_domain
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nemo
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epiviz-api
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README
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genomes
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hg19
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hg38
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