LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
cidc_schemas/__init__.py
cidc_schemas/cli.py
cidc_schemas/constants.py
cidc_schemas/json_validation.py
cidc_schemas/migrations.py
cidc_schemas/template.py
cidc_schemas/template_reader.py
cidc_schemas/template_writer.py
cidc_schemas/unprism.py
cidc_schemas/util.py
cidc_schemas/metaschema/strict_meta_schema.json
cidc_schemas/ngs_pipeline_api/__init__.py
cidc_schemas/ngs_pipeline_api/output_API.schema.json
cidc_schemas/ngs_pipeline_api/atacseq/atacseq.md
cidc_schemas/ngs_pipeline_api/atacseq/atacseq_output_API.json
cidc_schemas/ngs_pipeline_api/atacseq/imgs/atacseq.png
cidc_schemas/ngs_pipeline_api/rna/rna.md
cidc_schemas/ngs_pipeline_api/rna/rna_config.schema.json
cidc_schemas/ngs_pipeline_api/rna/rna_output_API.json
cidc_schemas/ngs_pipeline_api/rna/imgs/RIMA.png
cidc_schemas/ngs_pipeline_api/tcr/tcr.md
cidc_schemas/ngs_pipeline_api/tcr/imgs/TCRseq.png
cidc_schemas/ngs_pipeline_api/wes/wes.md
cidc_schemas/ngs_pipeline_api/wes/wes_config.schema.json
cidc_schemas/ngs_pipeline_api/wes/wes_output_API.json
cidc_schemas/ngs_pipeline_api/wes/wes_output_API.py
cidc_schemas/ngs_pipeline_api/wes/wes_tumor_only_output_API.json
cidc_schemas/ngs_pipeline_api/wes/imgs/wes.png
cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2
cidc_schemas/prism/__init__.py
cidc_schemas/prism/constants.py
cidc_schemas/prism/core.py
cidc_schemas/prism/extra_metadata.py
cidc_schemas/prism/merger.py
cidc_schemas/prism/pipelines.py
cidc_schemas/schemas/aliquot.json
cidc_schemas/schemas/clinical_data.json
cidc_schemas/schemas/clinical_trial.json
cidc_schemas/schemas/participant.json
cidc_schemas/schemas/sample.json
cidc_schemas/schemas/shipping_core.json
cidc_schemas/schemas/artifacts/artifact_bam.json
cidc_schemas/schemas/artifacts/artifact_bam_bai.json
cidc_schemas/schemas/artifacts/artifact_bed.json
cidc_schemas/schemas/artifacts/artifact_bigwig.json
cidc_schemas/schemas/artifacts/artifact_binary.json
cidc_schemas/schemas/artifacts/artifact_clinical_csv.json
cidc_schemas/schemas/artifacts/artifact_clinical_docx.json
cidc_schemas/schemas/artifacts/artifact_clinical_xlsx.json
cidc_schemas/schemas/artifacts/artifact_cncf.json
cidc_schemas/schemas/artifacts/artifact_cns.json
cidc_schemas/schemas/artifacts/artifact_core.json
cidc_schemas/schemas/artifacts/artifact_csv.json
cidc_schemas/schemas/artifacts/artifact_elisa_xlsx.json
cidc_schemas/schemas/artifacts/artifact_fastq_gz.json
cidc_schemas/schemas/artifacts/artifact_fcs.json
cidc_schemas/schemas/artifacts/artifact_file.json
cidc_schemas/schemas/artifacts/artifact_gz.json
cidc_schemas/schemas/artifacts/artifact_h5ad.json
cidc_schemas/schemas/artifacts/artifact_html.json
cidc_schemas/schemas/artifacts/artifact_ibd.json
cidc_schemas/schemas/artifacts/artifact_image.json
cidc_schemas/schemas/artifacts/artifact_imzml.json
cidc_schemas/schemas/artifacts/artifact_jpg.json
cidc_schemas/schemas/artifacts/artifact_json.json
cidc_schemas/schemas/artifacts/artifact_junction.json
cidc_schemas/schemas/artifacts/artifact_log.json
cidc_schemas/schemas/artifacts/artifact_maf.json
cidc_schemas/schemas/artifacts/artifact_mtx.json
cidc_schemas/schemas/artifacts/artifact_narrowPeak.json
cidc_schemas/schemas/artifacts/artifact_npx.json
cidc_schemas/schemas/artifacts/artifact_ome_tiff.json
cidc_schemas/schemas/artifacts/artifact_out.json
cidc_schemas/schemas/artifacts/artifact_parquet.json
cidc_schemas/schemas/artifacts/artifact_pdf.json
cidc_schemas/schemas/artifacts/artifact_png.json
cidc_schemas/schemas/artifacts/artifact_rcc.json
cidc_schemas/schemas/artifacts/artifact_rdata.json
cidc_schemas/schemas/artifacts/artifact_rds.json
cidc_schemas/schemas/artifacts/artifact_stats.json
cidc_schemas/schemas/artifacts/artifact_tab.json
cidc_schemas/schemas/artifacts/artifact_tbi.json
cidc_schemas/schemas/artifacts/artifact_text.json
cidc_schemas/schemas/artifacts/artifact_tiff.json
cidc_schemas/schemas/artifacts/artifact_tsv.json
cidc_schemas/schemas/artifacts/artifact_txt.json
cidc_schemas/schemas/artifacts/artifact_vcf.json
cidc_schemas/schemas/artifacts/artifact_vcf_gz.json
cidc_schemas/schemas/artifacts/artifact_xlsx.json
cidc_schemas/schemas/artifacts/artifact_yaml.json
cidc_schemas/schemas/artifacts/artifact_zip.json
cidc_schemas/schemas/assays/atacseq_assay.json
cidc_schemas/schemas/assays/ctdna_assay.json
cidc_schemas/schemas/assays/cytof_assay.json
cidc_schemas/schemas/assays/cytof_assay_core.json
cidc_schemas/schemas/assays/elisa_assay.json
cidc_schemas/schemas/assays/hande_assay.json
cidc_schemas/schemas/assays/ihc_assay.json
cidc_schemas/schemas/assays/maldi_glycan_assay.json
cidc_schemas/schemas/assays/mibi_assay.json
cidc_schemas/schemas/assays/microbiome_assay.json
cidc_schemas/schemas/assays/mif_assay.json
cidc_schemas/schemas/assays/mihc_assay.json
cidc_schemas/schemas/assays/misc_data.json
cidc_schemas/schemas/assays/nanostring_assay.json
cidc_schemas/schemas/assays/nulisa_assay.json
cidc_schemas/schemas/assays/olink_assay.json
cidc_schemas/schemas/assays/olink_ht_assay.json
cidc_schemas/schemas/assays/rna_assay-v0.json
cidc_schemas/schemas/assays/rna_assay.json
cidc_schemas/schemas/assays/scrnaseq_analysis.json
cidc_schemas/schemas/assays/scrnaseq_assay.json
cidc_schemas/schemas/assays/tcr_analysis.json
cidc_schemas/schemas/assays/tcr_assay.json
cidc_schemas/schemas/assays/tcrseq_rna_assay.json
cidc_schemas/schemas/assays/visium_analysis.json
cidc_schemas/schemas/assays/visium_assay.json
cidc_schemas/schemas/assays/wes_analysis.json
cidc_schemas/schemas/assays/wes_assay.json
cidc_schemas/schemas/assays/wes_core.json
cidc_schemas/schemas/assays/wes_tumor_only_analysis.json
cidc_schemas/schemas/assays/components/antibody.json
cidc_schemas/schemas/assays/components/assay_core.json
cidc_schemas/schemas/assays/components/available_assays.json
cidc_schemas/schemas/assays/components/available_ngs_analyses.json
cidc_schemas/schemas/assays/components/composite_image.json
cidc_schemas/schemas/assays/components/controls.json
cidc_schemas/schemas/assays/components/enrichment_core.json
cidc_schemas/schemas/assays/components/excluded_samples.json
cidc_schemas/schemas/assays/components/hande_local_file.json
cidc_schemas/schemas/assays/components/image.json
cidc_schemas/schemas/assays/components/imaging_data.json
cidc_schemas/schemas/assays/components/local_file.json
cidc_schemas/schemas/assays/components/maldi_glycan_input.json
cidc_schemas/schemas/assays/components/mapping.json
cidc_schemas/schemas/assays/components/mibi_antibody.json
cidc_schemas/schemas/assays/components/mif_antibody.json
cidc_schemas/schemas/assays/components/mihc_antibody.json
cidc_schemas/schemas/assays/components/mihc_input.json
cidc_schemas/schemas/assays/components/multiple_local_files.json
cidc_schemas/schemas/assays/components/ngs_assay_core.json
cidc_schemas/schemas/assays/components/ngs_assay_record.json
cidc_schemas/schemas/assays/components/nulisa_input.json
cidc_schemas/schemas/assays/components/reads_core.json
cidc_schemas/schemas/assays/components/reads_with_index.json
cidc_schemas/schemas/assays/components/scrnaseq_input.json
cidc_schemas/schemas/assays/components/scrnaseq_preamble.json
cidc_schemas/schemas/assays/components/visium_input.json
cidc_schemas/schemas/assays/components/visium_preamble.json
cidc_schemas/schemas/assays/components/imaging/mif_entry.json
cidc_schemas/schemas/assays/components/imaging/mif_export.json
cidc_schemas/schemas/assays/components/imaging/mif_input.json
cidc_schemas/schemas/assays/components/imaging/mif_roi.json
cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json
cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json
cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json
cidc_schemas/schemas/assays/components/ngs/rna/fusion.json
cidc_schemas/schemas/assays/components/ngs/rna/microbiome.json
cidc_schemas/schemas/assays/components/ngs/rna/msisensor.json
cidc_schemas/schemas/assays/components/ngs/rna/neoantigen.json
cidc_schemas/schemas/assays/components/ngs/rna/rna_analysis.json
cidc_schemas/schemas/assays/components/ngs/rna/rna_level1_analysis.json
cidc_schemas/schemas/assays/components/ngs/rna/rseqc.json
cidc_schemas/schemas/assays/components/ngs/rna/salmon.json
cidc_schemas/schemas/assays/components/ngs/rna/star.json
cidc_schemas/schemas/assays/components/ngs/rna/trust4.json
cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json
cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json
cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json
cidc_schemas/schemas/templates/analyses/scrnaseq_analysis_template.json
cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json
cidc_schemas/schemas/templates/analyses/visium_analysis_template.json
cidc_schemas/schemas/templates/analyses/wes_analysis_template.json
cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json
cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json
cidc_schemas/schemas/templates/assays/clinical_data_template.json
cidc_schemas/schemas/templates/assays/ctdna_template.json
cidc_schemas/schemas/templates/assays/cytof_template.json
cidc_schemas/schemas/templates/assays/elisa_template.json
cidc_schemas/schemas/templates/assays/hande_template.json
cidc_schemas/schemas/templates/assays/ihc_template.json
cidc_schemas/schemas/templates/assays/maldi_glycan_template.json
cidc_schemas/schemas/templates/assays/mibi_template.json
cidc_schemas/schemas/templates/assays/microbiome_template.json
cidc_schemas/schemas/templates/assays/mif_template.json
cidc_schemas/schemas/templates/assays/mihc_template.json
cidc_schemas/schemas/templates/assays/misc_data_template.json
cidc_schemas/schemas/templates/assays/nanostring_template.json
cidc_schemas/schemas/templates/assays/nulisa_template.json
cidc_schemas/schemas/templates/assays/olink_ht_template.json
cidc_schemas/schemas/templates/assays/olink_template.json
cidc_schemas/schemas/templates/assays/rna_bam_template.json
cidc_schemas/schemas/templates/assays/rna_fastq_template.json
cidc_schemas/schemas/templates/assays/scrnaseq_template.json
cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json
cidc_schemas/schemas/templates/assays/tcr_fastq_template.json
cidc_schemas/schemas/templates/assays/tcrseq_rna_template.json
cidc_schemas/schemas/templates/assays/visium_template.json
cidc_schemas/schemas/templates/assays/wes_bam_template.json
cidc_schemas/schemas/templates/assays/wes_fastq_template.json
cidc_schemas/schemas/templates/manifests/h_and_e_template.json
cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json
cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json
cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json
cidc_schemas/schemas/templates/manifests/pbmc_template.json
cidc_schemas/schemas/templates/manifests/plasma_template.json
cidc_schemas/schemas/templates/manifests/tissue_slide_template.json
cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json
cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json
cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json
nci_cidc_schemas.egg-info/PKG-INFO
nci_cidc_schemas.egg-info/SOURCES.txt
nci_cidc_schemas.egg-info/dependency_links.txt
nci_cidc_schemas.egg-info/entry_points.txt
nci_cidc_schemas.egg-info/not-zip-safe
nci_cidc_schemas.egg-info/requires.txt
nci_cidc_schemas.egg-info/top_level.txt
tests/__init__.py
tests/conftest.py
tests/constants.py
tests/test_artifacts.py
tests/test_assays.py
tests/test_clinicaltrial_examples.py
tests/test_json_validation.py
tests/test_migrations.py
tests/test_schemas.py
tests/test_strict_meta_schema.py
tests/test_template.py
tests/test_template_reader.py
tests/test_template_writer.py
tests/test_templates.py
tests/test_trial_core.py
tests/test_unprism.py
tests/test_util.py
tests/data/clinical_test_file.1.csv
tests/data/clinical_test_file.1.xlsx
tests/data/clinical_test_file.2.bom.csv
tests/data/clinical_test_file.2.csv
tests/data/clinical_test_file.2.xlsx
tests/data/clinical_test_file.3.xlsx
tests/data/clinical_test_file.docx
tests/data/date_examples.xlsx
tests/data/elisa_test_file.1.xlsx
tests/data/elisa_test_file.2.xlsx
tests/data/hande_err_template.xlsx
tests/data/pbmc_invalid.xlsx
tests/data/pbmc_manifest_valid.xlsx
tests/data/tiny_invalid_manifest.xlsx
tests/data/tiny_valid_manifest.xlsx
tests/data/clinicaltrial_examples/CT_1.json
tests/data/clinicaltrial_examples/CT_1PA_multiWES.json
tests/data/clinicaltrial_examples/CT_cytof_with_analysis.json
tests/data/clinicaltrial_examples/CT_ihc.json
tests/data/clinicaltrial_examples/CT_minimal.json
tests/data/olink/invalid_olink_assay_1_NPX.xlsx
tests/data/olink/olink_assay_1_NPX.xlsx
tests/data/olink/olink_assay_2_NPX.xlsx
tests/data/olink/olink_assay_combined.xlsx
tests/data/schemas/1.json
tests/data/schemas/a.json
tests/data/schemas/b.json
tests/data/schemas/c.json
tests/data/schemas/invalid_ref.json
tests/data/schemas/d1/3.json
tests/data/schemas/d1/d2/2.json
tests/data/schemas/target-templates/atacseq_analysis_template.json
tests/data/schemas/target-templates/rna_level1_analysis_template.json
tests/data/schemas/target-templates/wes_analysis_template.json
tests/data/schemas/target-templates/wes_tumor_only_analysis_template.json
tests/prism/__init__.py
tests/prism/test_cidc_data_model.py
tests/prism/test_constants.py
tests/prism/test_core.py
tests/prism/test_extra_metadata.py
tests/prism/test_merger.py
tests/prism/test_pipelines.py
tests/prism/cidc_test_data/__init__.py
tests/prism/cidc_test_data/analysis_data.py
tests/prism/cidc_test_data/assay_data.py
tests/prism/cidc_test_data/manifest_data.py
tests/prism/cidc_test_data/utils.py
tests/prism/schema/test_schema.json
tests/utils/test_template_generator.py