symphony

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is there a version for python?

1

I am a newer for R, is there a version for python users?

wubaosheng

Using counts matrix with known labels as reference

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Hi I would love to be able to try out `Symphony` for label-transfer, but with a set of labels defined by an alternative method to `Harmony`. So for example, starting...

wmacnair

Harmony with one variable having the same value for all cells

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Hi there, I am trying to build a reference based on tumor cells from this small cell lung cancer dataset, https://cellxgene.cziscience.com/collections/62e8f058-9c37-48bc-9200-e767f318a8ec. They calculated PCs based on MNN obtained with all...

YOU-k

I ran mapQuery and got the following error: `Error in exp_query[shared_genes, ] : subscript out of bounds` I manually repeated the steps from the function and noticed that up to...

schmeing

Hi, thank you for developing a great tool! I have a reference panel made by using scanpy and harmonypy, and considering performing query mapping of seurat objects using symphony. Do...

yyoshiaki

Reproducing a UMAP embedding with Symphony

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Hello, I wanted to use the mapQuery function on a UMAP generated from Harmony spaces by my regular pipeline. Then I saw in #15 that it wasn't implemented, so I...

yannk-lm

Error in checkna(X) : Missing values found in 'X' from mapQuery()

3

Dear Symphony Team, I got the following error message when I map the my query to my own reference. I appreciate your help: > query = mapQuery(query_exp , # query...

qicheng-ma

UMAP from reference is not transfered to samples - Symphony Seurat

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Dear Symphony Team, please excuse me opening another issue on this topic! Following your vignette (https://github.com/immunogenomics/symphony/blob/main/vignettes/Seurat.ipynb) i managed to run the complete script without errors (I rerun the RunHarmony.Seurat on...

NK-HD

Error when using Fibroblast atlas

3

Hi, I am trying to use the pre-built fibroblast atlas (https://sandbox.zenodo.org/record/772596#.YdRr5mDMIuV) in Symphony. I read in the RDS file as specified: fibroblast_reference sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-pc-linux-gnu (64-bit)...

jk86754

Symphony labels when query is a negative control

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Hello, I used Symphony to map two single-cell RNAseq queries to my harmony-integrated reference (made using the modular approach presented on Symphony Github). I used queries that were previously annotated...

hbandukw