IGEA is a web-based tool for integrative analysis of gene expression data.
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[DONE] Database
- schema to store Eperiment, Sample and Microarray metadata
- schema to store additional info on sample attribute names and values
- Store additional info on sample attribute standard names and values: link to ontologies (MeSh, EFO), explanation, synonyms
- [MOSTLY DONE] store and update in background Experiment status: standardized; mail sent, mail received, has minimal data for integration, is excluded etc.
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[DONE] Automate downloading metadata form ArrayExpress
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[DOING] Admin interface
- autocomplete lookup fields and "for each" checkboxes for easier input
- reduce loading form loading time
- samples metadata standardization form
- samples attribute add or replace form
- test data for duplicate entities
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[DOING] Deployment
- Deploy to Heroku hosting service; suspended due to exeeded space limit for a free account
- Deploy to the server at Institute of Molecular Biology and Genetics; accessible at http://194.44.31.241:24173/
- deploy to a server at European Grid Infrastructure
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[DONE] Data plots
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[DOING] Data access user interface
- Basic interface with header nav bar
- Experiments page with basic table of experiments
- Samples page with basic table of samples
- Upd tables with filter rows by column value
- [DOING] Side bar for Samples table to show/hide certain columns and rows with certain values
- Intro page
- Logo
- Downlowdable BibTex citations on nav bar
- [Х] Order columns properly
- [Х] Download Experiments, Samples tables as TSV files
- Upload Experiment, Sample metadata from TSV files provided by user
- Slider widgets to Samples side bar as search filters for numeric columns
- Exclude rows with empty values option
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Construct study groups based on metadata
- send study groups' meta- and expression data to Inmex
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Automate downloading and processing sample expression data from ArrayExpress
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Integrate sample expression data for study groups
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Search for differentially expressed genes.
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Embed earlier developed BNFinder tool for gene regulatory networks construction https://github.com/sysbio-vo/bnfinder/
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Data analysis user interface
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Embed Telegram bot featured for automated solving bioinformatican's minor problems, which is under development https://github.com/Dantistnfs/telegram-genetic-bot
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Specialized blog to quickly post new analysis results to IGEA site and to social media
- Python 3.5.2 - Programming language
- Django - Web develompent framework
- Postgres - Database
This project is licensed under the GNU General Public License - see the LICENSE file for details