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immunogenomics
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symphony
Efficient and precise single-cell reference atlas mapping with Symphony
GNU General Public License v3.0
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Question about mapQuery function
#51
MoLuLuMo
opened
1 month ago
0
Cannot use buildReferenceFromSeurat with RunHarmony v1.0.3
#50
dy-lin
opened
5 months ago
1
Error: Mat::init(): requested size is too large; suggest to enable ARMA_64BIT_WORD
#49
vivekruhela
opened
5 months ago
0
Cannot reproduce Seurat.ipynb vignette; parameters not passed
#48
Nichal123
opened
6 months ago
1
Query no longer projecting onto reference?
#47
cedmo001
closed
1 year ago
1
Transfer entire assay / expression matrix from reference onto query
#46
MalteThodberg
opened
1 year ago
0
Could this be used on multi-modality data, such as RNA+Protein data?
#45
JiahaoChow
closed
1 year ago
1
Seurat object with Harmony generate from PCA using specified features
#44
HarryShen668
closed
1 year ago
1
fix seurat reference if subset after harmony
#43
jiwen90
closed
1 year ago
0
L2 norm for cos distance for per cluster confidence score
#42
potulabe
opened
1 year ago
0
How to merge query and reference seurat objects?
#41
linusbiostat
opened
1 year ago
0
Fix for immunogenomics/symphony#39
#40
amcdavid
closed
1 year ago
0
calcPerClusterMappingMetric fails with singleton query_cluster_labels
#39
amcdavid
closed
1 year ago
0
Error in irlba(ref_exp_scaled, nv = 20)
#38
Lila3141
closed
1 year ago
1
Symphony update for R version 4.2.1
#37
mghanizada
closed
1 year ago
2
is there a version for python?
#36
wubaosheng
opened
2 years ago
1
Using counts matrix with known labels as reference
#35
wmacnair
opened
2 years ago
1
Harmony with one variable having the same value for all cells
#34
YOU-k
opened
2 years ago
1
Symphony crashes during mapQuery due to genes stored as factor in atlas
#33
schmeing
opened
2 years ago
0
Create reference using harmonypy results
#32
yyoshiaki
closed
1 year ago
2
Reproducing a UMAP embedding with Symphony
#31
yannk-lm
opened
2 years ago
1
Error in checkna(X) : Missing values found in 'X' from mapQuery()
#30
qicheng-ma
opened
2 years ago
2
Error message: in vargenes_vst
#29
qicheng-ma
closed
2 years ago
1
No plotBasic() defined in utils.R
#28
qicheng-ma
closed
2 years ago
1
Move some plot-"enhancing" packages to Suggests
#27
amcdavid
closed
2 years ago
0
Error message:"In split.default(seq_len(N), groups) : data length is not a multiple of split variable"
#26
qicheng-ma
closed
2 years ago
3
UMAP from reference is not transfered to samples - Symphony Seurat
#25
NK-HD
closed
1 year ago
2
How can I use your pipeline to annotate the in-house CITE-Seq query dataset with both scRNA-seq count matrix and ADT count matrix ?
#24
qicheng-ma
closed
2 years ago
0
Error when using Fibroblast atlas
#23
jk86754
opened
2 years ago
3
error: Mat::init(): requested size is too large
#22
plantformatics
closed
2 years ago
1
I can not find "exprs_norm_all.rds" and "meta_data_subtypes.csv" from data folder?
#21
holiday01
closed
2 years ago
3
Symphony labels when query is a negative control
#20
hbandukw
opened
2 years ago
5
argument confidence in knnPredict.Seurat
#19
klaramagdalena
closed
2 years ago
2
Does symphony provide corrected PCs like Harmony?
#18
albert-ying
closed
2 years ago
2
Seurat object as reference
#17
NK-HD
closed
2 years ago
8
One cluster in reference is completely missing in query predicted clusters - even when using a sample that was used for reference building
#16
florian0512
closed
1 year ago
2
load harmonized embeddings into harmony object for use with Symphony
#15
hbandukw
closed
2 years ago
1
Labels in Memory T Cell Atlas missing
#14
mihem
closed
2 years ago
8
Documentation typo
#13
GWW
closed
2 years ago
1
Choice of the value of the k parameter in the knnPredict function
#12
GAgafencu
closed
3 years ago
2
how top map the query to reference with prefix and postfix?
#11
Yale73
closed
2 years ago
2
Error in t.default(obj@reductions$harmony@misc$R) : argument is not a matrix
#10
dcruz5h
closed
3 years ago
3
How to build the symphony reference if the reference has no clear batch effect?
#9
Echo226
closed
3 years ago
2
Suggestion to update the new source code
#8
Yale73
closed
3 years ago
7
no slot of name "x" for this object of class "Seurat"
#7
Echo226
closed
3 years ago
4
Symphony installation question
#6
rach88
closed
3 years ago
3
could not find function "vargenes_vst"
#5
guanlinW
closed
3 years ago
3
prediction score
#4
padza21
closed
2 years ago
6
Question about finding variable genes with vst
#3
alitinet
closed
3 years ago
2
Error installing
#2
alitinet
closed
3 years ago
3
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