Joyce Kang comments

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                                            Joyce Kang

Symphony labels when query is a negative control

Hi! great question. As we discuss a bit in the paper, Symphony assumes the reference has the cell types you're interested in in the query. If there are "novel" cell...

Symphony labels when query is a negative control

Hi there, Thanks for trying out the confidence metric. It looks to me like the two distributions are indeed a bit different, since the IQR for the actual data is...

UMAP from reference is not transfered to samples - Symphony Seurat

Hi Niklas, Thanks for your message! I'm not entirely sure what is causing this error - would you mind trying it again but removing the confounding genes prior to the...

One cluster in reference is completely missing in query predicted clusters - even when using a sample that was used for reference building

Hi Florian, Thanks for the question. Trying to see if the issue is with the Symphony mapping procedure itself or how the reference was built. Would you be able to...

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

Hi Qicheng, Thanks for the message. Based on the output you listed, it looks like the `mapQuery` function is able to make it to the UMAP step before producing this...

Error when using Fibroblast atlas

Hi @jk86754 , Thanks for your message! Currently, the fibroblast atlas supports mapping to the atlas and label transfer (see https://github.com/immunogenomics/fibroblastatlas for tutorial). The fibroblast atlas may have been generated...

Using coloc for conditionally independent eQTLs in the HLA region

Hi Chris, thanks for the response. I have summary data (betas, varbetas, pvalues, LD if needed) as well as original genotypes. Is there a better way to do this that...

Reproducing a UMAP embedding with Symphony

Hi Yannick, Apologies for the delay in getting back to you. If you are still interested in tackling this, (1) the input to `harmony::HarmonyMatrix()` should be the uncorrected PCA matrix...

UMAP from reference is not transfered to samples - Symphony Seurat

Closing this issue, but feel free to reopen if still not resolved!

One cluster in reference is completely missing in query predicted clusters - even when using a sample that was used for reference building

Closing this issue (but feel free to reopen if still not resolved!)