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Please use the new version with latest annotation data iDEP 0.95.
Feb. 19, 2022: R upgraded from 4.05 to 4.1.2. This solved the STRING API issues. Some Bioconductor packages are also upgraded.
Feb. 11, 2022: Like iDEP but your genome is not covered? Customized iDEP is now available. Its database includes several custom genomes requested by users. To request to add new species/genome, fill in this Form.
Nov. 15, 2021: iDEP v0.95 released in testing mode. It includes Ensembl database update, new species from Ensembl Fungi and Ensembl Protists, and STRINGdb (5090 species) update from v11 to 11.5.
10/26/2021: The Genome view is now much improved! Automatically detects chromosomal regions enriched with genes having abnormaly high and low fold-changes.
iDEP v.0.94 based on Ensembl Release 104 and STRING-db V11. 9/3/2021
10/15/21: For GO enrichment analysis, we now recommend using background genes, instead of all genes on the genome. In the KNN and DEG2 tabs, it is now the default that all genes passed the filter in Pre-Process tab are used as a customized background.
We updated instruction for local installation here. The most recent database file is now publically available, free of charge for non-profit organizations.
Check out the 50,000+ datasets of uniformly processed public RNA-seq data here!
Email Jenny for questions. Dr. Ge is notorisly slow in responding to emails.
iDEP has not been thoroughly tested. Please let us know if you find any issue/bug.
10/18/20: Interactive network enables users to easily visualize the relatedness of pathways, similar to EnrichmentMap. Using the Network buttons on DEG2 and Pathway tabs, you can generate and export interactive networks like this one below. You can move the nodes by dragging them, zoom in by scrolling, and shift the entire network by click on an empty point and drag.