Error with import scvi in scRNA-seq with scanpy

Hi all,

I try to follow the tutorial below and get an error. https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb enter image description here

What is wrong in my case? Thank you so much!

Update: I figured it out.

scvi

• 662 views • link

written 3.8 years ago by Chris •

0 answers

No answers yet.

More posts like this

Help with single cell annotation
written 2.9 years ago by Chris •

Hi all, I am trying to do cell type annotation and got some difficulty. Automatically annotate using singleR is different than annotation using knowledge of …
How to choose threshold for scrublet?
written 3.0 years ago by bioinfo •

Hello, I am using scrublet to remove doublets from my data. I am following the tutorial here:https://github.com/swolock/scrublet/blob/master/examples/scrublet_basics.ipynb I don't think that the automatic threshold detection …
clustering using leiden algorithm
written 3.1 years ago by dalibenam64 •

Hello I'm trying to perform clustering on my data using scanpy. I used this tutorial: https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb My question is how I can store the plot …
About per tile sequence quality
written 3.2 years ago by Chris •

Hi all, I check a pair-end read sample and got this per tile sequence quality. ![enter image description here][1] ![enter image description here][2] Should I …
Positive and negative value fold value in ATAC seq using DiffBind
written 3.3 years ago by Chris •

Hi all, Does positive fold in this case mean the gene in diseased group is more accessible than the control group? The object is created …
How to fix "the kernel appears to have died. It will restart automatically."?
written 3.8 years ago by Chris •

Hi all, I follow this tutorial: https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb scvi.model.SCVI.setup_anndata(adata) vae = scvi.model.SCVI(adata) vae.train() "The kernel appears to have died. It will restart automatically." GPU available: False, …
How to fix attributeError: module 'scvi' has no attribute 'model'?
written 3.8 years ago by Chris •

Hi all, I try to follow the tutorial below and get an error. https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb Many people got the same error but the solution doesn't work …
Error with scanpy package on Jupyter notebook
written 3.9 years ago by Chris •

Hi all, I want to install a package name scanpy on Jupyter notebook so I run: `! pip3 install scanpy`, I got this: WARNING: You …
Trimmomatic - unknown trimmer?
written 4.8 years ago by liuhongran •

Hi, all I have Double End fastq file and it needs trimming. So, I use trimmomatic software for this purpose.based on trimmomatic tutorial I write …
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
written 5.3 years ago by Juke34

First install [AGAT][1]: ``` conda create -c bioconda -n agat agat conda activate agat ``` Then enjoy possibilities of `agat_sp_extract_sequences.pl`, below exemplified ![enter image description …