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Issues list

Question about the spatial/domains.ipynb question Further information is requested
#362 opened Apr 26, 2025 by 11e11
Ensure that PR previews also deploy on forked repositories bug Something isn't working
#359 opened Apr 22, 2025 by Zethson
@LuisHeinzlmeier
Proposing to add mLLMCelltype as a best practice for cell type annotation enhancement New feature or request
#354 opened Apr 18, 2025 by cafferychen777
@Zethson
6
Compatibility between simpleaf quant (spliceu mode) outputs and SoupX question Further information is requested
#350 opened Mar 26, 2025 by cave-beetle
question about Chapter16.4 Pseudobulk making code bug Something isn't working
#339 opened Feb 19, 2025 by dfc-1931475
1
Create a style guide enhancement New feature or request
#337 opened Feb 18, 2025 by LuisHeinzlmeier
@LuisHeinzlmeier
Missing yml files for every chapter/notebook enhancement New feature or request
#336 opened Feb 17, 2025 by LuisHeinzlmeier
File format chapter enhancement New feature or request
#334 opened Feb 15, 2025 by LuisHeinzlmeier
1
Verbosity Level bug Something isn't working
#332 opened Feb 14, 2025 by DarioS
1
Add SpatialData & squidpy tutorial to Analysis tools enhancement New feature or request
#330 opened Feb 7, 2025 by Zethson
1 of 6 tasks
@LuisHeinzlmeier
Adding tables + improve structure of strengths and limitations enhancement New feature or request
#328 opened Feb 4, 2025 by LuisHeinzlmeier
@LuisHeinzlmeier
1
Figure for UMI resolution enhancement New feature or request
#323 opened Feb 2, 2025 by LuisHeinzlmeier
@LuisHeinzlmeier
Outdated environemnt files bug Something isn't working
#319 opened Jan 20, 2025 by VladimirShitov
2
Issue on page /cellular_structure/integration.html
#308 opened Jan 5, 2025 by qinxiaoy
Issue on page /preprocessing_visualization/quality_control.html
#306 opened Nov 12, 2024 by jffpviana
Downstream analysis for sn-ATACseq is not shown in the contents? question Further information is requested
#304 opened Nov 10, 2024 by zyll123
Have hide-output and expandable cells enhancement New feature or request
#299 opened Sep 21, 2024 by Zethson
Filter rarely expressed genes/features? question Further information is requested
#298 opened Sep 17, 2024 by kloot
Question about the ambient RNA correction question Further information is requested
#296 opened Aug 22, 2024 by Chaosli98
1
Usage of pvals for volcano plots instead of FDR-corrected p-values question Further information is requested
#295 opened Aug 21, 2024 by ramadatta
SoupX: rowSums(data) : 'x' must be an array of at least two dimensions bug Something isn't working
#294 opened Aug 13, 2024 by Urja25
Nucleosome defaults
#288 opened Jul 25, 2024 by trev-f
@AnnaChristina
Better sorting of pathways in /conditions/gsea_pathway.html?
#287 opened Jul 24, 2024 by VladimirShitov
Update ATAC-seq section with: Benchmarking computational methods for single-cell chromatin data analysis enhancement New feature or request
#286 opened Jul 19, 2024 by ivirshup
@Zethson
1
Issue on page /mechanisms/gene_regulatory_networks.html about env and versions of packages
#285 opened Jul 18, 2024 by franvz9
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