TRON-Bioinformatics / covigator

CoVigator - Monitoring SARS-CoV-2 mutations

TRON-Bioinformatics/covigator Issues

Add table in home with features in each dataset
Closed 5 months ago
Update dash
Closed 7 months ago
Plot label and figure description are too close in the C19 Data Portal overview tab
Closed 7 months ago1
News section
Closed 7 months ago
Dashboard performance
Updated 7 months ago
Host_tax_id field is NA for all queried ENA runs
Updated 8 months ago1
Redesign intrahost tab
Updated 8 months ago
Integrate intrahost model into precomputations
Updated 8 months ago
Regenerate sklearn model
Updated 8 months ago
Make grey boxes on tabs clickable to highlight associated plot
Updated 8 months ago1
Search optimization of CoVigator dashboard with keywords
Closed 8 months ago1
The label "monthly frequencies" in the recurrent mutations table is incomplete (when choosing to show frequencies)
Closed 8 months ago1
Covid19Data Portal missing Lineages handling
Updated 9 months ago1
The date box on the top right of the page is overlapped by the tabs in small screens
Closed 9 months ago2
Edit the first paragraph in the landing page
Closed 9 months ago1
Can we make the need to click apply more explicit
Closed 9 months ago3
Add option in accessor to disable exclusion criteria based on minimum date
Closed 10 months ago1
Add option in accessor to disable exclusion criteria based on host_tax_id (as this is not always reported, eg: EBOV...)
Closed 10 months ago1
ENA API update
Closed 10 months ago2
Remove "effect" column from recurrent mutations table
Closed a year ago
Cite pangolin lineages in docs
Closed a year ago
Default time range to one year since last update (lineages and recurrent mutations tab)
Closed a year ago
Update constellation submodule (XBB lineages)
Closed a year ago
Implement a separate dashboard (ie: https://covigator.tron-mainz.de/lineages) accessible from the landing page
Updated a year ago
Update ENA accessor to include Nanopore data
Updated a year ago3
Update main system diagram in the documentation
Closed a year ago
Add reference to the preprint in CoVigator dashboard acknowledgements and in the documentation
Closed a year ago1
Annotate lineages with described mutations
Closed a year ago3
Lineage summary dashboard
Updated a year ago
Annotate lineages with names (eg: Delta)
Closed a year ago1
use lineages metadata to enrich the lineages plot in the dashboard
Closed a year ago
Hover tooltips in lineages plot are difficult to use
Closed a year ago1
Capture feedback from the dashboard
Closed a year ago1
Data download returns 404 for low_frequency_variant_observation and lq_clonal_variant_observation
Closed a year ago3
In the intrahost tab the selection of mutations to expand details requires clicking apply and running expensive queries again, this could be seperated to an independent buttom "view details"
Updated a year ago
Add some teaser info on each tab
Closed a year ago
Avoid possible SQL injections by using placeholders
Closed a year ago
Change VAF range in intrahost tab to include VAFs below 10 %
Closed a year ago
Harmonize colors of mutations in legends in mutation stats tab
Closed a year ago
Add exclusion criteria for sample without collection date
Updated a year ago
Prepare proposal of plots and information to show (slide-based)
Updated a year ago1
Frequencies are not segregated by months in the recurrent mutations table
Closed a year ago
Some monthly frequencies are slightly above 1.0 in table precomputed_top_occurrence
Closed a year ago
Change threshold for low frequency mutations to 2 % and store mutations >= 50 % and < 80 % in different table
Closed a year ago
Smooth the lineages plot
Closed a year ago
Implement the intrahost mutations filter on dashboard
Closed a year ago
Search bar for lineages
Updated a year ago
Link to the lineage summary (eg: https://covigator.tron-mainz.de/lineages/B.1.1.7) from the lineages tab of other dashboards
Updated a year ago
Implement a simplistic lineage selection with a dropdown box that opens the page of the selected lineage
Updated a year ago
Implement content of the dashboard
Updated a year ago