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chanzuckerberg
/
galago
Interpretation aids for genomic epidemiology
https://chanzuckerberg.github.io/galago/
MIT License
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Light up descendent internal nodes on mrca hover
#60
sidneymbell
opened
2 years ago
0
Copy edits in light of new role of "selected samples" -> "optionally highlighted samples"
#59
sidneymbell
closed
2 years ago
0
Mock of interactions w/ PHI/PII
#58
sidneymbell
closed
2 years ago
0
Require "unpin" click before re-enabling mrca hovering
#57
sidneymbell
closed
2 years ago
0
Visually distinguish "important" samples in scatterplot
#56
sidneymbell
closed
2 years ago
0
Color scatterplot by metadata
#55
sidneymbell
closed
2 years ago
0
Change size of mrca dots relative to proportion of "highlight samples" included in their descendents
#54
sidneymbell
closed
2 years ago
0
Debug hover states after sample highlighting
#53
sidneymbell
closed
2 years ago
0
Light up samples in scatterplot on mrca hover
#52
sidneymbell
closed
2 years ago
0
Where possible, change sampling bias table to "samples within X mutations of one of your selected samples"
#51
sidneymbell
opened
2 years ago
0
Make it clear which samples are part of the same / separate transmission chain(s)
#50
sidneymbell
opened
2 years ago
1
Running list of questions it would be helpful to answer in a potential future "cluster detection" report
#49
sidneymbell
closed
2 years ago
0
Running list of questions it would be helpful to answer in a potential future "sample level" report
#48
sidneymbell
closed
2 years ago
0
Add a "recommended next steps" section to each insight
#47
sidneymbell
opened
2 years ago
0
Sampling bias table should show "neighboring counties," not just "other counties in your state"
#46
sidneymbell
opened
2 years ago
0
Pull in incidence data --> snapshot of % sequenced over time (i.e., what's the sampling frame of the contextual data)
#45
sidneymbell
opened
2 years ago
0
"How to use this report" video
#44
sidneymbell
opened
2 years ago
0
Provide CA-specific guidance on how to link genomic data with CalREDIE investigations
#43
sidneymbell
closed
2 years ago
1
Provide guidance on how much contextual data is "enough"
#42
sidneymbell
opened
2 years ago
0
Provide guidance on when to expand the scope of an investigation when there are many "cousin" samples
#41
sidneymbell
closed
2 years ago
0
Provide guidance on how this information should be used, esp wrt presentations / papers
#40
sidneymbell
closed
2 years ago
2
Add contingency table for other metadata fields vs clade membership
#39
sidneymbell
closed
2 years ago
0
Split off "tree utils" -> ETE-JS partial port package
#38
sidneymbell
opened
2 years ago
0
Re-attempt MDX 2.0 integration
#37
sidneymbell
opened
2 years ago
0
Validate which surveillance-relevant data is available / where
#36
sidneymbell
closed
2 years ago
0
Enable users to compare "clustering" results from trimming deep nodes vs nextstrain ancestral states vs matutils
#35
sidneymbell
closed
2 years ago
0
Make context counts responsive to date range in tree
#34
sidneymbell
closed
2 years ago
0
Add user inputs for report parameters
#33
sidneymbell
closed
2 years ago
0
Add user inputs for remaining report parameters
#32
sidneymbell
closed
2 years ago
0
Brainstorm initial designs for inline plots
#31
sidneymbell
closed
2 years ago
0
Test with output from ClusterTracker --> scope work needed for interoperability
#30
sidneymbell
opened
2 years ago
0
Provide a demo dataset
#29
sidneymbell
closed
2 years ago
0
Export as nextstrain narratives?
#28
sidneymbell
opened
2 years ago
0
Plug in example data from Humboldt paper
#27
sidneymbell
closed
2 years ago
0
Add names of samples upon request / user click
#26
sidneymbell
closed
2 years ago
0
Add additional context sentence(s) to each insight. Final copy edits.
#25
sidneymbell
closed
2 years ago
0
Define what data needs to be surfaced in surveillance report
#24
sidneymbell
closed
2 years ago
0
Fix alignment of sidenotes
#23
sidneymbell
closed
2 years ago
0
Add insight re: variants / lineages in these samples
#22
sidneymbell
closed
2 years ago
0
Add inline heatmap for "how closely related are your samples to each other"
#21
sidneymbell
closed
2 years ago
2
Alphabetize and unique-ize location data points
#20
sidneymbell
closed
2 years ago
0
"What are clusters? How is this different from clades?"
#19
sidneymbell
closed
2 years ago
0
Move insight components to MDX so that other scientists and users can easily contribute updates to narratives
#18
sidneymbell
closed
2 years ago
0
deploy to some subdomain so test users can access it
#17
sidneymbell
closed
2 years ago
0
Add insight on phylogenetic uncertainty
#16
sidneymbell
opened
2 years ago
1
Incorporate preliminary expert feedback from Alli and Mikala
#15
sidneymbell
closed
2 years ago
0
Enable skimming through clades via a "max N descendents" slider that yields exploded subtrees by pruning off deep nodes
#14
sidneymbell
closed
2 years ago
0
Fix text formatting for arrays embedded in `{`${my_array}`}`
#13
sidneymbell
closed
2 years ago
0
Add an epi curve visual for the clade of interest
#12
sidneymbell
closed
2 years ago
0
Epi curve visual for timeline + metadata distributions
#11
sidneymbell
closed
2 years ago
2
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