fix-list.md

IRIS Bug Fixes

Cankun

• Add new data set (large scRNA) to BMBL server
• Install ape package
• Install Rtsne package
• Install WGCNA package
• Install MCL package
• Install kmed package
• Install flashClust package
• Install parallel package
• Work on MCL algorithm pipeline

Brandon

• Disconnect from server single-cell data count summary - large data
• Color palettes for Discovery-Driven Analysis tab
• Windows 7 issues - Cankun
• Eliminate gene list load option from scRNA 10X selection
• Update tutorial and supplementary file with new functionalities
• Integrate MCL clustering algorithm
• Fix tutorial TOC links
• Fix scRNA user loading bug
• Integrate scRNA - 10X option into start page
• Add tutorial statement to Submit & QC page
• WGCNA - add sample download button
• t-SNE option - add download options
• kmed - add download options
• Integrate kmed clustering algorithm
• WGCNA - add download options
• Integrate WGCNA clustering algorithm
• Fix MDS image download bugs
• t-SNE option - add 2d and 3d option
• t-SNE option - use Rtsne package
• t-SNE option - add perplexity parameter
• Fix download filtered DGE data bug
• No plots appear on DGE analysis when there are zero DEGs
• Fix GEO metadata download error
• Fix GEO zip file download error
• Update tutorial
• Add Dr. Fennell to About Us tab
• Summary data formatting
• Error in single-cell DGE
• Fix code in tutorial for downloading local app

Reviewers (PLOS Computational Biology)

• Integrate new clustering methods (MCL)
• Integrate scRNA - 10X option into start page
• Integrate new clustering methods (WGCNA)
• Integrate new clustering methods (kmed)
• Add t-SNE tab to Discovery Driven Analysis
• Create static page discussing functional enrichment