Introduction
DataHub is part of RGC-AoE Center for Genomic Studies on Plant Environment Interaction (GSPEI) Central Data Portal project, aiming to provide a fast and convenient way for biologists to access and utilize soybean genomics data.
Main features
- Flexible gene search function
- Including four high-quality soybean reference geenomes which are most frequently used
- Updated gene functional annotation with interproscan
- Integrated BLAST service with varies of options
- Multiple genomics datasets re-analyzed and illustrated in Jbrowse
- Pair-wise synteny blocks identified and visualization
- Easy to use sequence extraction tools with batch entry supported
- Primer design integrated for search result, with clear visualization for both the primer and restriction enzyme sites
Release Note
AoE DataHub updates 04/02/2024
- JBrowse2 was integrated into the app
AoE DataHub updates 11/11/2021
- Gene expression could be accessed as barplot in gene search tab
AoE DataHub updates 10/10/2021
- Integrated miRNA expression as heatmap to the gene search result, 8 datasets for Gmax_a4v1 were added.
- Various genomic datasets were added to Jbrowse section, updated list could be viewed here.
AoE DataHub updates 30/07/2021
- Integrated annotation from UniProt/Swiss-Prot database
- Added support for illustrating InterProScan discovered domain result
AoE DataHub updates 16/07/2021
- Documents were online
AoE DataHub updates 29/06/2021
- Synteny Blocks among genomes were analyzed by MCScan and visualization section was integrated.
AoE DataHub updates 22/05/2021
- Flanking sequence could be extracted from gene search tabs.
AoE DataHub 0.0.4 released 18/05/2021
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Added primer design function with primer3 as a backend.
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REBASE (20210430) was integrated.
AoE DataHub 0.0.3 released 15/01/2021
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All the data of four genomes were populated.
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Jbrowse content was updated for new added genomes.
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All genes were reannotated with latest version of interproscan 5.48-83.0.
AoE DataHub 0.0.2 released 10/01/2021
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Sequence Extractor function added.
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BLAST function improved, much faster than before.
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Application UI modified.
AoE DataHub 0.0.1 released 24/11/2020
- This is the testing version of prototype, and this section is for release content testing only. For prototype, we added data for W05 only, the BLAST function and Jbrowse was integrated to the shiny dashboard app.