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Query annotation hub for populating the TxDB registry. (#5)
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‎CHANGELOG.md‎

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# Changelog
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## Version 0.0.1 - 0.0.3
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## Version 0.0.1 - 0.0.4
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- Initial release of the package with class structure and basic functionality.
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- Fixed minor bugs handling existing resources with cache.
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- Download and cache Annotation Hub's sqlite metadata file for querying available TxDB objects.

‎src/txdb/_ahub.py‎

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__copyright__ = "Jayaram Kancherla"
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__license__ = "MIT"
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TXDB_CONFIG = {
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"TxDb.Athaliana.BioMart.plantsmart22": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Athaliana.BioMart.plantsmart22.sqlite",
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},
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"TxDb.Athaliana.BioMart.plantsmart25": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Athaliana.BioMart.plantsmart25.sqlite",
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},
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"TxDb.Athaliana.BioMart.plantsmart28": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Athaliana.BioMart.plantsmart28.sqlite",
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},
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"TxDb.Btaurus.UCSC.bosTau8.refGene": {
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"release_date": "2020-10-20",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Btaurus.UCSC.bosTau8.refGene.sqlite",
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},
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"TxDb.Celegans.UCSC.ce11.refGene": {
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"release_date": "2019-05-01",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Celegans.UCSC.ce11.refGene.sqlite",
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},
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"TxDb.Celegans.UCSC.ce6.ensGene": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Celegans.UCSC.ce6.ensGene.sqlite",
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},
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"TxDb.Cfamiliaris.UCSC.canFam3.refGene": {
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"release_date": "2020-10-20",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Cfamiliaris.UCSC.canFam3.refGene.sqlite",
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},
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"TxDb.Dmelanogaster.UCSC.dm3.ensGene": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Dmelanogaster.UCSC.dm3.ensGene.sqlite",
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},
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"TxDb.Dmelanogaster.UCSC.dm6.ensGene": {
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"release_date": "2020-10-20",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Dmelanogaster.UCSC.dm6.ensGene.sqlite",
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},
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"TxDb.Drerio.UCSC.danRer10.refGene": {
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"release_date": "2019-05-01",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Drerio.UCSC.danRer10.refGene.sqlite",
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},
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"TxDb.Ggallus.UCSC.galGal4.refGene": {
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"release_date": "2020-10-20",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Ggallus.UCSC.galGal4.refGene.sqlite",
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},
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"TxDb.Hsapiens.BioMart.igis": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Hsapiens.BioMart.igis.sqlite",
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},
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"TxDb.Hsapiens.UCSC.hg18.knownGene": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Hsapiens.UCSC.hg18.knownGene.sqlite",
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},
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"TxDb.Hsapiens.UCSC.hg19.knownGene": {
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"release_date": "2025-10-29",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.22/TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite",
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},
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"TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts.sqlite",
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},
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"TxDb.Hsapiens.UCSC.hg38.knownGene": {
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"release_date": "2025-10-29",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.22/TxDb.Hsapiens.UCSC.hg38.knownGene.sqlite",
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},
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"TxDb.Hsapiens.UCSC.hg38.refGene": {
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"release_date": "2024-04-02",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.19/TxDb.Hsapiens.UCSC.hg38.refGene.sqlite",
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},
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"TxDb.Mmulatta.UCSC.rheMac3.refGene": {
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"release_date": "2020-10-20",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Mmulatta.UCSC.rheMac3.refGene.sqlite",
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},
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"TxDb.Mmulatta.UCSC.rheMac8.refGene": {
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"release_date": "2020-10-20",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Mmulatta.UCSC.rheMac8.refGene.sqlite",
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},
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"TxDb.Mmulatta.UCSC.rheMac10.refGene": {
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"release_date": "2021-10-08",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.14/TxDb.Mmulatta.UCSC.rheMac10.refGene.sqlite",
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},
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"TxDb.Mmusculus.UCSC.mm10.ensGene": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Mmusculus.UCSC.mm10.ensGene.sqlite",
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},
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"TxDb.Mmusculus.UCSC.mm10.knownGene": {
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"release_date": "2019-05-01",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite",
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},
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"TxDb.Mmusculus.UCSC.mm39.refGene": {
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"release_date": "2024-04-02",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.19/TxDb.Mmusculus.UCSC.mm39.refGene.sqlite",
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},
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"TxDb.Mmusculus.UCSC.mm39.knownGene": {
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"release_date": "2025-03-11",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.21/TxDb.Mmusculus.UCSC.mm39.knownGene.sqlite",
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},
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"TxDb.Mmusculus.UCSC.mm9.knownGene": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Mmusculus.UCSC.mm9.knownGene.sqlite",
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},
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"TxDb.Ptroglodytes.UCSC.panTro4.refGene": {
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"release_date": "2020-04-27",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Ptroglodytes.UCSC.panTro4.refGene.sqlite",
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},
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"TxDb.Ptroglodytes.UCSC.panTro5.refGene": {
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"release_date": "2020-04-27",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Ptroglodytes.UCSC.panTro5.refGene.sqlite",
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},
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"TxDb.Ptroglodytes.UCSC.panTro6.refGene": {
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"release_date": "2019-10-29",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.10/TxDb.Ptroglodytes.UCSC.panTro6.refGene.sqlite",
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},
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"TxDb.Rnorvegicus.BioMart.igis": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Rnorvegicus.BioMart.igis.sqlite",
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},
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"TxDb.Rnorvegicus.UCSC.rn4.ensGene": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Rnorvegicus.UCSC.rn4.ensGene.sqlite",
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},
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"TxDb.Rnorvegicus.UCSC.rn5.refGene": {
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"release_date": "2020-04-27",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Rnorvegicus.UCSC.rn5.refGene.sqlite",
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},
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"TxDb.Rnorvegicus.UCSC.rn6.refGene": {
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"release_date": "2019-05-01",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Rnorvegicus.UCSC.rn6.refGene.sqlite",
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},
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"TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq": {
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"release_date": "2020-10-20",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq.sqlite",
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},
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"TxDb.Rnorvegicus.UCSC.rn7.refGene": {
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"release_date": "2022-04-18",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.15/TxDb.Rnorvegicus.UCSC.rn7.refGene.sqlite",
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},
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"TxDb.Scerevisiae.UCSC.sacCer2.sgdGene": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene.sqlite",
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},
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"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene": {
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"release_date": "2016-12-22",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene.sqlite",
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},
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"TxDb.Sscrofa.UCSC.susScr3.refGene": {
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"release_date": "2020-04-27",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Sscrofa.UCSC.susScr3.refGene.sqlite",
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},
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"TxDb.Sscrofa.UCSC.susScr11.refGene": {
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"release_date": "2020-04-27",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Sscrofa.UCSC.susScr11.refGene.sqlite",
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},
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"TxDb.Ggallus.UCSC.galGal5.refGene": {
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"release_date": "2020-04-27",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Ggallus.UCSC.galGal5.refGene.sqlite",
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},
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"TxDb.Ggallus.UCSC.galGal6.refGene": {
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"release_date": "2019-10-29",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.10/TxDb.Ggallus.UCSC.galGal6.refGene.sqlite",
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},
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"TxDb.Cfamiliaris.UCSC.canFam4.refGene": {
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"release_date": "2021-10-08",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.14/TxDb.Cfamiliaris.UCSC.canFam4.refGene.sqlite",
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},
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"TxDb.Cfamiliaris.UCSC.canFam5.refGene": {
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"release_date": "2021-10-08",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.14/TxDb.Cfamiliaris.UCSC.canFam5.refGene.sqlite",
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},
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"TxDb.Cfamiliaris.UCSC.canFam6.refGene": {
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"release_date": "2023-04-06",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.17/TxDb.Cfamiliaris.UCSC.canFam6.refGene.sqlite",
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},
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"TxDb.Celegans.UCSC.ce11.ensGene": {
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"release_date": "2022-04-18",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.15/TxDb.Celegans.UCSC.ce11.ensGene.sqlite",
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},
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"TxDb.Drerio.UCSC.danRer11.refGene": {
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"release_date": "2019-05-01",
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"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Drerio.UCSC.danRer11.refGene.sqlite",
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},
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}
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AHUB_METADATA_URL = "https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3"

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