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Hi,
Thank you for your work with Palantir. I have been running into issues with
`imputed_X = palantir.utils.run_magic_imputation(ad,n_jobs=16)`
(or any n_jobs > 1).
I get the following wa…
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Dear authors of cellphoneDB, first of all, thanks for this very very useful tool!
I am using it to evaluate ligand-receptor interactions among different annotated cell type a scRNAseq dataset.
I am …
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I'm trying to use `rapidsai/rapidsai-core:22.02-cuda11.5-base-ubuntu20.04-py3.8` docker image for this competition. But the conda environment to use in this docker image is `rapids` instead of `base`.…
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Error reported by Tianyu going through the answer key notebooks
My concern is about the content in the colab code of workshop Batch correction in PBMCs (Answer Key)
I find that there are some err…
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Hello,
I'm trying to create a new loom file after making edits to an existing one (the adult mouse brain dataset from [Mousebrain.org](http://mousebrain.org/downloads.html),`L5_All.loom ` ).
H…
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Hello,
I'm currently trying to read in a h5ad-file into R. Since seurats ReadH5ad()-function didn't work out for me, I tried to do it with seurat-disk. First I converted my file into a h5seurat-fil…
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- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of scanpy.
- [X] (optional) I have confirmed this bug exists on the m…
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Hi,
I'm trying to use `diffxpy` with an AnnData object that has been clustered using the Leiden algorithm.
When I run the following command:
`wilcox_test = de.test.wilcoxon(data = batches_…
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>>> corrected = mnnpy.mnn_correct(a,b,var_index=gene, var_subset=hvgs, batch_categories = ["A", "B"], cos_norm_out=False)
Inputs are AnnData objects, var_index ignored.
Performing cosine normalizati…
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It seems that somehow MANIFESTS are not getting the cell_to_library lines written even though studies do have cell_to_library.txt files within the bundle:
```
(miniconda3)[host results]$ ls -l */*…
pcm32 updated
2 years ago