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emdann
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milopy
Python implementation of Milo for differential abundance testing on KNN graph
MIT License
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Using different latent space and knn for milo analysis
#48
revolvefire
opened
1 month ago
2
milo.DA_nhoods "ValueError" covariates cannot be unambiguously assgined to each sample
#47
quiquevb23
closed
1 month ago
2
error with milo.count_nhoods(adata, sample_col="sample")
#46
yebo085
closed
6 months ago
2
Fix 'X' was used for kNN
#45
canergen
closed
10 months ago
1
milo.make_nhoods(combined_emb) fails if 'X' was used for nearest neighbors
#44
canergen
closed
10 months ago
1
make_nhoods Error: Mean of empty slice.
#43
jflusche
opened
11 months ago
2
Fix annotate_nhoods
#42
emdann
closed
1 year ago
0
annotate_nhood error
#41
ali-harasty
closed
1 year ago
2
DA_nhoods() .iteritems deprecated
#40
james-cranley
closed
1 year ago
3
convert annotation_labels to list at time of storing
#39
ktpolanski
closed
1 year ago
1
plotNhoodExpressionDA in milopy?
#38
ilibarra
opened
1 year ago
0
Fixed lib_size filtering in DA_nhoods
#37
emdann
closed
1 year ago
0
Bug: errors if no cells covered for a certain sample
#36
emdann
closed
1 year ago
0
Interpret the clustering result
#35
ZhenjiangFan
closed
1 year ago
2
Error in make_nhoods if the reduced dims are in pandas.DataFrame
#34
emdann
opened
1 year ago
1
AttributeError: recarray has no attribute columns
#33
PGmajev
opened
1 year ago
0
Get all cells of a neighborhood given the index_cell
#32
vronii-k
closed
1 year ago
2
Assigning neighbors_key in milopy.core.make_nhoods
#31
ghost
closed
1 year ago
1
Misc bug fixes
#30
emdann
closed
1 year ago
0
Where can I find the information about to which neighborhood a cell belongs
#29
ZhenjiangFan
closed
1 year ago
2
Error in glmFit.default(sely, design, offset = seloffset, dispersion = 0.05, : nrow(design) disagrees with ncol(y)
#28
Mari123i
closed
1 year ago
2
Fix breaking change to SpatialFDR with pandas 1.5
#27
emdann
closed
1 year ago
0
Refactoring with MuData
#26
emdann
opened
2 years ago
5
trying a new test
#25
emdann
closed
2 years ago
0
bump to v0.1.0
#24
emdann
closed
2 years ago
0
Merge branch 'master' of github.com:emdann/milopy into devel
#23
emdann
closed
2 years ago
0
autoapi
#22
emdann
closed
2 years ago
0
building API
#21
emdann
closed
2 years ago
0
fixing bug in vscode-notebook kernelspec
#20
emdann
closed
2 years ago
0
updated docs requirements
#19
emdann
closed
2 years ago
0
updated conf for rtd
#18
emdann
closed
2 years ago
0
added sphinx docs
#17
emdann
closed
2 years ago
0
Misc plotting improvements and small fixes
#16
emdann
closed
2 years ago
0
fixed intercept issue when specifying contrasts
#15
emdann
closed
2 years ago
0
fix error when specifying KNN graph key
#14
emdann
closed
2 years ago
0
Add informative error when running plot_nhood_graph before graph construction
#13
emdann
opened
2 years ago
0
Adding I/O utils and some small fixes
#12
emdann
closed
2 years ago
0
ValueError: Length mismatch
#11
DunxinShen
closed
2 years ago
2
Small fixes for subsetting and future proofing
#10
emdann
closed
2 years ago
0
added function to aggregate continuous variables on nhoods
#9
emdann
closed
2 years ago
0
Fixing conversion breaking DA_nhoods with rpy2>=3.5
#8
emdann
closed
2 years ago
0
plotNhoodGraphDA in python version
#7
alitinet
closed
2 years ago
4
Retrieving adata.obs_names belonging to each adata.uns["nhood_adata"].obs_names
#6
castaway1990
closed
2 years ago
3
Unable to save adata.uns["nhood_adata"]
#5
jan-domke
closed
2 years ago
2
Can't use model.contrasts with categorical variables
#4
emdann
closed
2 years ago
2
added option to set contrasts in DA testing
#3
emdann
closed
2 years ago
0
Native python implementation for NB-GLM instead of `edgeR`
#2
emdann
opened
3 years ago
9
Fix DA_nhoods warning from rpy2
#1
emdann
closed
1 year ago
0