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zdebruine
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singlet
Single-cell analysis with non-negative matrix factorization
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Error in if (rank_ind == nrow(df_rep)) { : argument is of length zero
#54
ElyasMo
opened
2 months ago
0
Adds ability to run nmf with new method
#53
skyler-ruiter
opened
4 months ago
0
Extracting barcodes per component
#52
kmh005
opened
5 months ago
3
Clarification on input for NMF -- raw counts or normalized data?
#51
stephaniehicks
closed
5 months ago
4
RunLNMF error: "memory not mapped"
#50
MicTott
opened
5 months ago
0
cross_validate_nmf giving NAN tolerance and overfit
#49
cindyfang70
opened
5 months ago
2
Compilation Error on Installation
#48
samuel-marsh
opened
5 months ago
10
Compatibility with Seurat V5
#47
zdebruine
opened
5 months ago
1
Advice for usage of Linked NMF for scATAC
#46
IsaacDiaz026
closed
6 months ago
1
Coerce w and h to matrices when rank=1 (closes #44)
#45
knowah
closed
6 months ago
0
run_nmf() fails with rank=1
#44
knowah
closed
6 months ago
0
Error in if (k_init < k_min) stop("k_init cannot be less than k_min"): argument is of length zero
#43
ryanhchung
closed
6 months ago
5
split.by option in RunNMF
#42
IsaacDiaz026
closed
6 months ago
1
Singlet modifies the original data matrix in the Seurat object
#41
TaopengWang
closed
6 months ago
13
Revert "My PR"
#40
zdebruine
closed
8 months ago
0
Issue with RunNMF on SeuratV5 objects
#39
jemorlanes
closed
6 months ago
12
My PR
#38
SBaluszek
closed
8 months ago
0
Update run_nmf.R
#37
SBaluszek
closed
8 months ago
0
c_nmf needs number of threads
#36
SBaluszek
closed
8 months ago
2
RunGSEA getting stuck at 8%
#35
Prathyusha-konda
closed
9 months ago
3
MetadataPlot needs to drop factor levels with 0 counts
#34
zdebruine
opened
10 months ago
0
Fix AnnotateNMF() bug
#33
ttriche
closed
10 months ago
0
cleanup and add coercions
#32
ttriche
closed
11 months ago
1
Corner case of RunNMF trying rank 1
#31
MarcElosua
closed
6 months ago
3
AnnotateNMF() does not pass internal checks
#30
zdebruine
closed
10 months ago
2
remove scuttle dependency
#29
ttriche
closed
1 year ago
1
added tests, made ProjectData work on SingleCellExperiment objects, added documentation
#28
ttriche
closed
1 year ago
0
Rlog1p error
#27
jemorlanes
closed
1 year ago
8
RunGSEA(pbmc3k,verbose = FALSE) gives empty results using example data
#26
rosaranli
closed
1 year ago
3
class "nmf" is not exported by 'namespace:RcppML'
#25
shalbahl
closed
10 months ago
8
fix transpose bug
#24
ttriche
closed
1 year ago
0
cleaned up getModelMatrix and getModelFit with new examples for testing
#23
ttriche
closed
1 year ago
0
getModelFit throwing error regarding dimnames
#22
zdebruine
closed
1 year ago
4
Updated procrustes and Rescaled NMF
#21
Barthur006
closed
7 months ago
1
"Not a matrix." error when it's definitely a matrix
#20
Wainberg
closed
1 year ago
6
Fixed a couple of missing/extra variable bugs
#19
Wainberg
closed
1 year ago
0
Rescaled and Procrutes
#18
Barthur006
closed
1 year ago
0
Silence protip
#17
ttriche
closed
1 year ago
0
added a few more convenience methods for nmf objects
#16
ttriche
closed
1 year ago
1
refactored, added list -> nmf coercion for ard_nmf results, etc.
#15
ttriche
closed
1 year ago
2
Option to select features for NMF
#14
ludvigla
closed
1 year ago
2
Fixed k for RunNMF
#13
ludvigla
closed
1 year ago
2
ard_nmf crashes on segfault (problem occurs in c_nmf_base) for dense data matrix
#12
ttriche
closed
1 year ago
1
Fix Seurat issue (retain full functionality for nmf, data.frame, and SCE objects)
#11
ttriche
closed
1 year ago
0
fix bug where factors with negative lods could still be included in AnnotationPlot output
#10
ttriche
closed
1 year ago
0
refactored AnnotateNMF to accept a list of design matrices, center and/or scale factor matrix, etc.
#9
ttriche
closed
1 year ago
0
Importing RcppML in NAMESPACE but not DESCRIPTION
#8
zdebruine
closed
1 year ago
2
force model fits to annotate against grand means
#7
ttriche
closed
1 year ago
1
RunNMF() error - if (overfit_score == 0) cat(" not overfit\n")
#6
dpcook
closed
1 year ago
2
Fixed a buglet in AnnotationPlot and implemented matrix pvalue-to-fdr correction for AnnotateNMF
#5
ttriche
closed
1 year ago
1
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