LICENSE
MANIFEST.in
README.md
deploy.sh
docs.sh
lint.sh
mkdocs.yml
pyproject.toml
test.sh
docs/catalogs.md
docs/copy-yeast.md
docs/coverage.md
docs/dog-peptides.md
docs/examples.md
docs/human-tissue.md
docs/index.md
docs/ingolia-yeast.md
docs/measurements.md
docs/pairing.md
docs/pfizer-protein.md
docs/pfizer-rna.md
docs/proteome.md
docs/reference.md
docs/search-references.md
docs/source-references.md
docs/species.md
docs/storage.md
docs/viral.md
docs/stylesheets/docs.css
orfdata/__init__.py
orfdata/_pinned_genome.py
orfdata/_structure.py
orfdata/build.py
orfdata/catalog.py
orfdata/catalog_cli.py
orfdata/catalog_manifest.py
orfdata/catalogs.py
orfdata/cli.py
orfdata/dataset.py
orfdata/dataset_cli.py
orfdata/datasets.py
orfdata/evidence.py
orfdata/evidence_summary.py
orfdata/genomes.py
orfdata/genomes_cli.py
orfdata/initiation_context.py
orfdata/install.py
orfdata/liftover.py
orfdata/liftover_cli.py
orfdata/measurements.py
orfdata/model.py
orfdata/pairing.py
orfdata/proteome.py
orfdata/proteome_cli.py
orfdata/reference.py
orfdata/reference_mapping.py
orfdata/refseq.py
orfdata/rna.py
orfdata/search_reference.py
orfdata/sequence.py
orfdata/version.py
orfdata/viral.py
orfdata.egg-info/PKG-INFO
orfdata.egg-info/SOURCES.txt
orfdata.egg-info/dependency_links.txt
orfdata.egg-info/entry_points.txt
orfdata.egg-info/requires.txt
orfdata.egg-info/top_level.txt
orfdata/data/catalogs.json
orfdata/data/chains.json
orfdata/data/datasets.json
orfdata/data/genomes.json
orfdata/data/ires/rfam-15.1-human-ires.json
orfdata/data/orf-evidence/AUTHOR-LICENSE.txt
orfdata/data/orf-evidence/NOTICE.txt
orfdata/data/orf-evidence/catalog.json.gz
orfdata/data/orf-evidence/manifest.json
orfdata/data/uorf-evidence/AUTHOR-LICENSE.txt
orfdata/data/uorf-evidence/NOTICE.txt
orfdata/data/uorf-evidence/catalog.json.gz
orfdata/data/uorf-evidence/manifest.json
orfdata/data/viral/NOTICE.md
orfdata/data/viral/hpv16-refseq-CDS.json.gz
orfdata/sources/__init__.py
orfdata/sources/copy.py
orfdata/sources/ingolia.py
orfdata/sources/kaabinejadian.py
orfdata/sources/ncorf_mammals.py
orfdata/sources/openprot.py
orfdata/sources/peptideatlas.py
orfdata/sources/pfizer.py
orfdata/sources/pfizer_rna.py
orfdata/sources/riborf.py
orfdata/sources/wang.py
tests/conftest.py
tests/test_catalog_registry.py
tests/test_copy.py
tests/test_cross_reference_pairing.py
tests/test_dog_peptides.py
tests/test_ensembl_search_reference.py
tests/test_evidence_rules.py
tests/test_evidence_summary.py
tests/test_genetic_codes.py
tests/test_genomes.py
tests/test_ingolia.py
tests/test_initiation_context.py
tests/test_liftover.py
tests/test_local_build_queries.py
tests/test_measurements.py
tests/test_merge_catalogs.py
tests/test_more_species.py
tests/test_ncorf_mammals.py
tests/test_openprot.py
tests/test_orf_cases.py
tests/test_paired_selectors.py
tests/test_pairing.py
tests/test_pfizer.py
tests/test_pfizer_rna.py
tests/test_proteome.py
tests/test_reference_context.py
tests/test_reference_mapping.py
tests/test_reference_orf.py
tests/test_refseq.py
tests/test_region_targets.py
tests/test_riborf.py
tests/test_search_reference.py
tests/test_selectors.py
tests/test_storage.py
tests/test_uorf_catalog.py
tests/test_viral.py
tests/test_wang.py
tests/data/aggregate_evidence.json
tests/data/copy/GSM1905474.soft
tests/data/copy/GSM1905474_KL9_fpkm.txt.gz
tests/data/copy/GSM1905476.soft
tests/data/copy/GSM1905476_KL10_fpkm.txt.gz
tests/data/copy/GSM1905478.soft
tests/data/copy/GSM1905478_KL11_fpkm.txt.gz
tests/data/copy/GSM1905479.soft
tests/data/copy/GSM1905479_KL12_fpkm.txt.gz
tests/data/copy/NOTICE.md
tests/data/copy/expected.json
tests/data/copy/geo-series.soft
tests/data/copy/manifest.json
tests/data/copy/methods.pdf
tests/data/copy/paper.xml
tests/data/copy/pmc-metadata.json
tests/data/copy/qconcat.fasta
tests/data/copy/workbook.xlsx
tests/data/ingolia/GSM346111.metadata.txt
tests/data/ingolia/GSM346111.quant.txt.gz
tests/data/ingolia/GSM346114.metadata.txt
tests/data/ingolia/GSM346114.quant.txt.gz
tests/data/ingolia/GSM346115.metadata.txt
tests/data/ingolia/GSM346115.quant.txt.gz
tests/data/ingolia/GSM346116.metadata.txt
tests/data/ingolia/GSM346116.quant.txt.gz
tests/data/ingolia/GSM346117.metadata.txt
tests/data/ingolia/GSM346117.quant.txt.gz
tests/data/ingolia/GSM346118.metadata.txt
tests/data/ingolia/GSM346118.quant.txt.gz
tests/data/ingolia/GSM346120.metadata.txt
tests/data/ingolia/GSM346120.quant.txt.gz
tests/data/ingolia/GSM346122.metadata.txt
tests/data/ingolia/GSM346122.quant.txt.gz
tests/data/ingolia/NOTICE.md
tests/data/ingolia/expected.json
tests/data/ingolia/manifest.json
tests/data/ingolia/readMe.txt.gz
tests/data/kaabinejadian/README.md
tests/data/kaabinejadian/Results.zip
tests/data/kaabinejadian/manifest.json
tests/data/kaabinejadian/sdrf.tsv
tests/data/ncorf_mammals/README.md
tests/data/ncorf_mammals/S3.xlsx
tests/data/ncorf_mammals/ensembl107.cdna.fa.gz
tests/data/ncorf_mammals/ensembl107.gtf.gz
tests/data/ncorf_mammals/human-ensembl107.gtf.gz
tests/data/ncorf_mammals/human.bed
tests/data/ncorf_mammals/human.pep.fa
tests/data/ncorf_mammals/mouse.bed
tests/data/ncorf_mammals/mouse.pep.fa
tests/data/openprot/README.md
tests/data/openprot/ensembl106.cdna.fa.gz
tests/data/openprot/ensembl106.gtf.gz
tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.bed.zip
tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.fasta.zip
tests/data/openprot/mouse-openprot-2_2-altprots+isoforms-min_2_pep-GRCm39.106.tsv.zip
tests/data/peptideatlas/README.md
tests/data/peptideatlas/atlas_build.tsv.zip
tests/data/peptideatlas/ensembl.pep.fa.gz
tests/data/peptideatlas/manifest.json
tests/data/pfizer/NOTICE.md
tests/data/pfizer/dog/expected.json
tests/data/pfizer/dog/manifest.json
tests/data/pfizer/dog/protein.tsv
tests/data/pfizer/dog/search.fasta
tests/data/pfizer/human/expected.json
tests/data/pfizer/human/manifest.json
tests/data/pfizer/human/protein.tsv
tests/data/pfizer/human/search.fasta
tests/data/pfizer/mouse/expected.json
tests/data/pfizer/mouse/manifest.json
tests/data/pfizer/mouse/protein.tsv
tests/data/pfizer/mouse/search.fasta
tests/data/pfizer_rna/GSE325522_family.soft.gz
tests/data/pfizer_rna/GSE325523_family.soft.gz
tests/data/pfizer_rna/GSE325525_family.soft.gz
tests/data/pfizer_rna/NOTICE.md
tests/data/pfizer_rna/counts.csv.gz
tests/data/pfizer_rna/dog-annotation.gtf.gz
tests/data/pfizer_rna/dog-expected.json
tests/data/pfizer_rna/dog-manifest.json
tests/data/pfizer_rna/mouse-annotation.gtf.gz
tests/data/pfizer_rna/mouse-expected.json
tests/data/pfizer_rna/mouse-manifest.json
tests/data/pfizer_rna/samples.xlsx
tests/data/references/README.md
tests/data/references/canis_lupus_familiaris.json
tests/data/references/context-keys-v0.4.json
tests/data/references/ensembl115.json
tests/data/references/homo_sapiens.json
tests/data/references/mitochondrial.json
tests/data/references/mus_musculus.json
tests/data/references/saccharomyces_cerevisiae.json
tests/data/references/uniprot_literature.json
tests/data/regions/NOTICE.md
tests/data/regions/ingolia.json
tests/data/riborf/README.md
tests/data/riborf/SD3.xlsx
tests/data/riborf/ensembl107.cdna.fa.gz
tests/data/riborf/ensembl107.gtf.gz
tests/data/riborf/ensembl107.ncrna.fa.gz
tests/data/riborf/human-ensembl105.cdna.fa.gz
tests/data/riborf/human-ensembl105.gtf.gz
tests/data/riborf/human-ensembl105.ncrna.fa.gz
tests/data/riborf/worm-ensembl105.cdna.fa.gz
tests/data/riborf/worm-ensembl105.gtf.gz
tests/data/riborf/worm-ensembl105.ncrna.fa.gz
tests/data/riborf/yeast-ensembl115.cdna.fa.gz
tests/data/riborf/yeast-ensembl115.dna.fa.gz
tests/data/riborf/yeast-ensembl115.gtf.gz
tests/data/riborf/zebrafish-ensembl115.cdna.fa.gz
tests/data/riborf/zebrafish-ensembl115.gtf.gz
tests/data/riborf/zebrafish-ensembl115.ncrna.fa.gz
tests/data/search_reference/NOTICE.md
tests/data/search_reference/dog.fasta
tests/data/search_reference/ensembl83-expected.json
tests/data/search_reference/ensembl83-human.fasta.gz
tests/data/search_reference/expected.json
tests/data/storage/README.md
tests/data/storage/generate.py
tests/data/storage/v1.json
tests/data/storage/v1.sqlite
tests/data/storage/v2.json
tests/data/storage/v2.sqlite
tests/data/storage/v3.json
tests/data/storage/v3.sqlite
tests/data/storage/v4.json
tests/data/storage/v4.sqlite
tests/data/viral/NC_001526.4.gb.gz
tests/data/wang/NOTICE.md
tests/data/wang/annotation.gtf.gz
tests/data/wang/copies.zip
tests/data/wang/expected.json
tests/data/wang/manifest.json
tests/data/wang/protein.zip
tests/data/wang/rna.zip
tests/data/wang/search.fasta.gz
tools/__init__.py
tools/build_hpv16_cds.py