Fabiola Curion

dsc-pileup zcat vcf

1

as seen here https://github.com/statgen/popscle/wiki For dsc-pileup, is it mandatory if the VCF is compressed to specify the parameter as --vcf

Hi, I need to demultiplex a pooled sample where the genotype of all but 2 individuals is known. How should I feed this into the demultiplexing pipeline? I thought of...

QC of deconvoluted SNG

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I've run 2 big experiments with demultiplexing so far. Both of them have unsatisfying SNG numbers compared to the expected numbers from the publication and for sure less than 90%...

version of demuxlet that does not require external genotypes

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Hi, about a year ago @hyunminkang mentioned that there would have been an upgrade on the genotyping strategy. It seems nothing has happened (?) Has anyone tried genotyping on 10x...

Hi Christopher, we'd like to reproduce Fig 4C. What is each point overlaid on violins? - Average geneset x cell? therefore, the distribution's mean is the mean of the geneset?...

multiVI fails with invalid tensor

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Hi scvi team, thanks for the excellent tools! I'm reaching out with an issue running MultiVI with versions scvi-tools >=0.20.3 the error is the same reported [here](https://discourse.scverse.org/t/error-when-training-model-on-m3-max-mps/1896/2) and [here](https://discourse.scverse.org/t/macbook-m1-m2-mps-acceleration-with-scvi/2075/4). i...

WriteH5MU fails

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Hi, thanks for working on interoperability between seurat and mudata! I am failing to save the [seurat object ](https://atlas.fredhutch.org/data/nygc/multimodal/pbmc_multimodal.h5seurat) offered in this [tutorial](https://satijalab.org/seurat/articles/multimodal_reference_mapping.html#computing-an-spca-transformation-1) ``` reference sessionInfo() R version 4.1.2 (2021-11-01)...

I've tested the patch but I still see the same error. Strangely, the error disappears upon forcing my ADT matrix to a sparse matrix using `Seurat::as.sparse`. Now I can load my `mudata` file.

5

> I've tested the patch but I still see the same error. Strangely, the error disappears upon forcing my ADT matrix to a sparse matrix using `Seurat::as.sparse`. Now I can...

sc.tl.umap on custom connectivities from representation "X" forces PCA calc instead

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I am calculating custom connectivities using hsnw on rep 'X', I don't want to calculate PCA, I want to compute UMAP using these connectivities. sc.tl.umap falls back to pca in:...

Hi, which scanpy version has the normalize_geometric function for citeseq data? I'm running: ``` sc.logging.print_versions() scanpy==1.5.2.dev24+g83844013 anndata==0.7.3 umap==0.4.4 numpy==1.18.5 scipy==1.4.1 pandas==1.0.5 scikit-learn==0.23.1 statsmodels==0.11.1 ``` thanks!