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In this file https://github.com/hbctraining/scRNA-seq_online/blob/master/lessons/04_SC_quality_control.md either the description or formula should be corrected, because `log10(x/y) = log10(x) - log10(…
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Hi,
I have a naïve question regarding the workflow of CellphoneDB.
From the web portal, it is stated that "the mean of the average receptor expression level in a cluster and the average ligand exp…
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Hello,
Firstly, thank you for creating this package and the accompanying benchmarking paper. The paper has been an invaluable resource for myself and colleagues over the past year!
I have been t…
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Hello dear fellows,
I met an error when I am running snakepipes ATAC_seq workflow, based on the log file it's like:
1. Can not activating conda environment `/opt/anaconda/miniconda3/envs/37c86fa5…
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Hello it's me again 😄
So I've tried to continue my grouped and integrated analysis using only 2 samples and during both steps **Int_Clust_Markers_Annot_GE** and **Grp_Clust_Markers_Annot_GE** afte…
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Dear all,
in the case of a project with few cells in a sc-RNA-seq dataset, I am getting the same error as in:
https://github.com/satijalab/seurat/issues/1914
I'm correcting it via editing the…
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scv.pl.scatter cannot generate plot to show transcriptional switches.
I convert seurat object to anndata, and then perform rna velocity (dynamical model) through scVelo. I can generate the heatmap …
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I'm integrating 5' RNA-seq and TCR data, works well thanks. One question, `adata[adata.obs["has_ir"] == "False"].obs["clonotype"]` includes unique categories for each cell in the form `"n_5_no IR"`, a…
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Hi @pmelsted ,
I also commented this question on a closed issue but not sure if those are monitored:
https://github.com/pachterlab/kallisto/issues/207
I have a question about the meaning of the…
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Hi Seurat group,
Thanks for developing such a powerful and user-friendly tool.
See the attached figure. I have one sc-RNAseq data and one scATAC-seq data. Both of them have a strong batch effec…