immunogenomics symphony issues

immunogenomics / symphony

Efficient and precise single-cell reference atlas mapping with Symphony

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Question about mapQuery function

#51 MoLuLuMo opened 3 months ago
0
Cannot use buildReferenceFromSeurat with RunHarmony v1.0.3

#50 dy-lin opened 8 months ago
1
Error: Mat::init(): requested size is too large; suggest to enable ARMA_64BIT_WORD

#49 vivekruhela opened 8 months ago
0
Cannot reproduce Seurat.ipynb vignette; parameters not passed

#48 Nichal123 opened 9 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 2 years 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
3
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 3 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 3 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 3 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