AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
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.egg-info/PKG-INFO
cidc_schemas.egg-info/SOURCES.txt
cidc_schemas.egg-info/dependency_links.txt
cidc_schemas.egg-info/entry_points.txt
cidc_schemas.egg-info/not-zip-safe
cidc_schemas.egg-info/requires.txt
cidc_schemas.egg-info/top_level.txt
cidc_schemas/metaschema/strict_meta_schema.json
cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2
cidc_schemas/pipeline_configs/wes_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_trial.json
cidc_schemas/schemas/collection_event.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_binary.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_gz.json
cidc_schemas/schemas/artifacts/artifact_image.json
cidc_schemas/schemas/artifacts/artifact_json.json
cidc_schemas/schemas/artifacts/artifact_maf.json
cidc_schemas/schemas/artifacts/artifact_npx.json
cidc_schemas/schemas/artifacts/artifact_tbi.json
cidc_schemas/schemas/artifacts/artifact_text.json
cidc_schemas/schemas/artifacts/artifact_tsv.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_zip.json
cidc_schemas/schemas/assays/cytof_assay.json
cidc_schemas/schemas/assays/elisa_assay.json
cidc_schemas/schemas/assays/ihc_assay.json
cidc_schemas/schemas/assays/micsss_assay.json
cidc_schemas/schemas/assays/mif_assay.json
cidc_schemas/schemas/assays/olink_assay.json
cidc_schemas/schemas/assays/rna_assay.json
cidc_schemas/schemas/assays/wes_assay.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/fastq_pair_or_bam.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/mapping.json
cidc_schemas/schemas/assays/components/micsss_antibody.json
cidc_schemas/schemas/assays/components/mif_antibody.json
cidc_schemas/schemas/assays/components/multiple_local_files.json
cidc_schemas/schemas/assays/components/ngs_assay_core.json
cidc_schemas/schemas/assays/components/cytof/cytof_analysis.json
cidc_schemas/schemas/assays/components/cytof/cytof_antibody.json
cidc_schemas/schemas/assays/components/cytof/cytof_entry.json
cidc_schemas/schemas/assays/components/cytof/cytof_input.json
cidc_schemas/schemas/assays/components/elisa/elisa_antibody.json
cidc_schemas/schemas/assays/components/imaging/ihc_antibody.json
cidc_schemas/schemas/assays/components/imaging/ihc_entry.json
cidc_schemas/schemas/assays/components/imaging/ihc_input.json
cidc_schemas/schemas/assays/components/imaging/micsss_entry.json
cidc_schemas/schemas/assays/components/imaging/micsss_input.json
cidc_schemas/schemas/assays/components/imaging/mif_entry.json
cidc_schemas/schemas/assays/components/imaging/mif_input.json
cidc_schemas/schemas/assays/components/imaging/mif_roi.json
cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json
cidc_schemas/schemas/assays/components/ngs/rna/rna_entry.json
cidc_schemas/schemas/assays/components/ngs/rna/rnaseq_analysis.json
cidc_schemas/schemas/assays/components/ngs/rna/rnaseq_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/wes/alignment.json
cidc_schemas/schemas/assays/components/ngs/wes/clonality.json
cidc_schemas/schemas/assays/components/ngs/wes/copynumber.json
cidc_schemas/schemas/assays/components/ngs/wes/corealignments.json
cidc_schemas/schemas/assays/components/ngs/wes/coverage_metrics.json
cidc_schemas/schemas/assays/components/ngs/wes/germline.json
cidc_schemas/schemas/assays/components/ngs/wes/neoantigen.json
cidc_schemas/schemas/assays/components/ngs/wes/optitype.json
cidc_schemas/schemas/assays/components/ngs/wes/purity.json
cidc_schemas/schemas/assays/components/ngs/wes/report.json
cidc_schemas/schemas/assays/components/ngs/wes/somatic.json
cidc_schemas/schemas/assays/components/ngs/wes/wes_analysis.json
cidc_schemas/schemas/assays/components/ngs/wes/wes_entry.json
cidc_schemas/schemas/assays/components/ngs/wes/wes_pair_analysis.json
cidc_schemas/schemas/assays/components/ngs/wes/wes_sample_analysis.json
cidc_schemas/schemas/assays/components/olink/olink_combined.json
cidc_schemas/schemas/assays/components/olink/olink_entry.json
cidc_schemas/schemas/assays/components/olink/olink_input.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/wes_analysis_template.json
cidc_schemas/schemas/templates/manifests/h_and_e_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
cidc_schemas/schemas/templates/metadata/cytof_template.json
cidc_schemas/schemas/templates/metadata/elisa_template.json
cidc_schemas/schemas/templates/metadata/ihc_template.json
cidc_schemas/schemas/templates/metadata/mif_template.json
cidc_schemas/schemas/templates/metadata/olink_template.json
cidc_schemas/schemas/templates/metadata/rna_bam_template.json
cidc_schemas/schemas/templates/metadata/rna_fastq_template.json
cidc_schemas/schemas/templates/metadata/wes_bam_template.json
cidc_schemas/schemas/templates/metadata/wes_fastq_template.json
tests/__init__.py
tests/conftest.py
tests/constants.py
tests/test_artifacts.py
tests/test_assays.py
tests/test_clinicaltrial_examples.py
tests/test_generate_docs.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/date_examples.xlsx
tests/data/elisa_test_file.xlsx
tests/data/pbmc_invalid.xlsx
tests/data/pbmc_shipping.xlsx
tests/data/tiny_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/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/prism/__init__.py
tests/prism/test_cidc_data_model.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