x-atlas-consortia hra-pop issues

x-atlas-consortia / hra-pop

HRApop

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refactor: :sparkles: Adjust how similarities are computed

#93 bherr2 opened 1 day ago
1
Adjust how `similarities` are computed

#92 andreasbueckle opened 1 week ago
0
2 atlas SenNet datasets do not show values in `cell_type_annotation_tool`

#91 andreasbueckle opened 3 weeks ago
2
Dashboard graphs for hra-pop

#90 andreasbueckle opened 1 month ago
0
Add `developmental_stage` to the graph in the next HRA release (post 2.1)

#89 andreasbueckle opened 1 month ago
0
Need atlas and non-atlas data for Sankey diagram

#88 andreasbueckle opened 1 month ago
0
Add column with whether CT is in ASCT+B Table

#87 andreasbueckle closed 1 month ago
2
Query for UBERON IDs and HRA DOs

#86 andreasbueckle closed 1 month ago
2
Use hra-3d-cell-generation API to build cell type visualization for one organ for companion website

#85 andreasbueckle closed 2 months ago
1
Need unique list of assay types in 9223 universe datasets

#84 andreasbueckle closed 2 months ago
2
One more report for AS and CT pairs

#83 andreasbueckle closed 2 months ago
4
Initial config and data

#82 axdanbol closed 2 months ago
0
Add disclaimer: Some atlas extraction sites do not have mesh collisions

#80 andreasbueckle opened 3 months ago
0
New long table for UMAP plot for biomarkers

#79 andreasbueckle opened 3 months ago
1
Make EUI for hra-pop atlas datasets

#78 andreasbueckle closed 2 months ago
3
`skin` and `skin of body` as `as_label` in v2p1

#77 andreasbueckle opened 3 months ago
1
Compile CSVs for validation with UMAP plots

#76 andreasbueckle closed 2 months ago
0
Make report for datasets with unsupported organs

#75 andreasbueckle opened 3 months ago
0
As `as_label` to v2p1 query

#74 andreasbueckle closed 2 months ago
1
Rename `sc_bulk` and `spatial`

#73 andreasbueckle closed 3 months ago
0
Need report for datasets with <100 cells

#72 andreasbueckle opened 3 months ago
1
Check if extraction site sets need to be renamed

#71 andreasbueckle opened 4 months ago
0
Make new UMAP plots for validation

#70 andreasbueckle opened 4 months ago
0
From how many different collections do the hra-pop level CxG datasets come from?

#69 andreasbueckle closed 4 months ago
1
Write new query for cells and Bs

#68 andreasbueckle opened 4 months ago
0
Compile overview of donor demographics for Universe

#67 andreasbueckle closed 4 months ago
1
Fix all extraction sites without mesh collision

#66 andreasbueckle opened 4 months ago
0
Fix registration on VHM back right arm (no mesh collision detected)

#65 andreasbueckle opened 4 months ago
0
Pbi test azimuth portal vs atlas input

#64 andreasbueckle closed 4 months ago
0
Update ER diagram

#63 andreasbueckle opened 4 months ago
0
Implement feedback on Fig. ASHeteroHomo

#62 andreasbueckle closed 4 months ago
1
In Fig. ValidationApplicationResults, add bars and jitter with number of AS per organ (plus other changes, see print-out)

#61 andreasbueckle opened 4 months ago
0
Address changes requested by Katy in REPORTS.md

#60 bherr2 opened 4 months ago
0
Identify duplicate cells between secondary datasets in CxG

#59 andreasbueckle closed 3 months ago
1
Verify number of datasets from CxG Portal

#58 andreasbueckle closed 2 months ago
0
Move text from old manuscript to new, clean one

#57 andreasbueckle opened 4 months ago
0
Add sparql query + results documentation

#56 bherr2 closed 5 months ago
0
Changed queries to point to universe

#55 andreasbueckle closed 5 months ago
0
Reorganized queries into subfolders

#54 bherr2 closed 5 months ago
1
Rename figs semantically, determine order later

#53 andreasbueckle closed 4 months ago
0
Investigate publishing ```test-atlas-enriched-dataset-graph``` using DVC

#52 andreasbueckle closed 5 months ago
1
Check if Tabula Sapiens is in ```full-dataset-graph```

#51 andreasbueckle closed 5 months ago
1
Document hra-pop queries in Markdown file

#50 andreasbueckle closed 2 months ago
3
Visualize validation and application reports

#49 andreasbueckle opened 5 months ago
0
Separate reports into ```atlas``` and ```ad_hoc```

#48 andreasbueckle closed 5 months ago
0
Need table for cell types per organ per tool

#47 andreasbueckle closed 4 months ago
1
New vis: scatter plot where each dot = 1 AS, x => avg cosine sim, y = number of datasets, color = organ

#46 andreasbueckle opened 5 months ago
0
Need total of 3D AS and for how many have hra-pop (by sex, laterality)

#45 andreasbueckle opened 5 months ago
1
Total number of cells in ```spatial-and-bulk-datasets-breakdown.csv``` is too low

#44 andreasbueckle closed 2 months ago
0
Visualize predictions by organ (validation-2+), then check against hetero-homogeneity

#43 andreasbueckle opened 5 months ago
0