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Lotfollahi-lab
/
nichecompass
End-to-end analysis of spatial multi-omics data
https://nichecompass.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
32
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6
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Problem creating NicheCompass model
#74
styounes
closed
6 days ago
2
Update package version and release notes
#73
sebastianbirk
closed
3 weeks ago
0
Revision
#72
sebastianbirk
closed
3 weeks ago
0
Kernel crashing when training the model with an adata (Visium HD) with 600k bins
#71
Rafael-Silva-Oliveira
closed
1 month ago
7
_compute_connectivities_umap
#70
mossishahi
closed
1 month ago
1
Compatibility with Visium HD data (8 micron)
#69
Rafael-Silva-Oliveira
closed
1 month ago
4
move scglue to optional dependency
#68
adamrboxall
closed
2 months ago
0
installation requires pybedtools
#67
adamrboxall
closed
2 months ago
0
MERFISH sample without GPs
#66
Dana162001
closed
4 months ago
9
ValueError: max() arg is an empty sequence [Error during the model training]
#65
hkeremcil
closed
3 months ago
6
Can I run NicheCompass with zebrafish Visium data?
#64
hkeremcil
closed
5 months ago
4
Cannot replicate the result in the multimodal_tutorials
#63
dyxmvp
closed
3 weeks ago
3
Tutorials review
#62
ArianAmani
closed
6 months ago
0
Change data type of latent representation to improve scaling
#61
sebastianbirk
closed
6 months ago
0
Status badges
#60
ArianAmani
closed
6 months ago
0
clustering requires manual downstream processing, but is resource intensive
#59
adamrboxall
closed
3 weeks ago
0
no way to export mu and std for active gps from the model conveniently
#58
adamrboxall
closed
3 weeks ago
0
reference-query training cannot be performed with mismatched gene coverage
#57
adamrboxall
closed
3 weeks ago
0
GP annotations files missing
#56
Eneritz
closed
8 months ago
0
add simple model evaluation
#55
adamrboxall
closed
3 weeks ago
0
50 add cli
#54
adamrboxall
closed
7 months ago
1
deployment on HPC environments is difficult due to compatibility issues
#53
adamrboxall
closed
3 weeks ago
0
Feature/communication network rework
#52
irene-bonapa
closed
7 months ago
0
reduce repo size
#51
adamrboxall
closed
7 months ago
0
add CLI to wrap 'reproducibility' scripts
#50
adamrboxall
closed
3 weeks ago
0
add minimal tests
#49
adamrboxall
closed
3 weeks ago
0
refactor run configuration
#48
adamrboxall
closed
7 months ago
0
46 add devcontainer
#47
adamrboxall
closed
9 months ago
3
fix compatibility issues for development
#46
adamrboxall
closed
9 months ago
0
CLean up gp summary retrieval
#45
sebastianbirk
closed
1 year ago
0
Backup/after addon redesign
#44
sebastianbirk
closed
1 year ago
0
Feature/decoder redesign
#43
sebastianbirk
closed
1 year ago
0
Bugfix/l1 mask
#42
sebastianbirk
closed
1 year ago
0
Feature/cat covariates
#41
sebastianbirk
closed
1 year ago
0
Feature/gp mask rework
#40
sebastianbirk
closed
1 year ago
0
Complete rebranding
#39
sebastianbirk
closed
1 year ago
0
Feature/atac analysis capabilities
#38
sebastianbirk
closed
1 year ago
0
Feature/atac seq multimodal model
#37
sebastianbirk
closed
1 year ago
0
Feature/atac seq multimodal model
#36
sebastianbirk
closed
1 year ago
0
Modify negative edge sampling to discard edges across conditions
#35
sebastianbirk
closed
1 year ago
0
Feature/cosine sim decoder
#34
sebastianbirk
closed
1 year ago
0
Feature/agg attention weight retrieval
#33
sebastianbirk
closed
1 year ago
0
Feature/denovo gps
#32
sebastianbirk
closed
1 year ago
0
Feature/query mapping
#31
sebastianbirk
closed
1 year ago
0
Feature/query mapping
#30
sebastianbirk
closed
1 year ago
0
Dev
#29
sebastianbirk
closed
1 year ago
0
Improvements in latent representation retrieval
#28
sebastianbirk
closed
1 year ago
0
Benchmarking of active gene programs
#27
sebastianbirk
closed
1 year ago
0
Add node-level mse computation
#26
sebastianbirk
closed
1 year ago
0
Add mebocost gps
#25
sebastianbirk
closed
1 year ago
0
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