Tag: SCVI

scRNA seq integration 1 Hello, I’m working on different replicate of 2 types of conditions (patients and control ) my question : should we created a seurat object for each replicate and don’t merge then and then apply the normlization and batch effect seperately or we merge 2 conditions and…

Scanpy and SCVI help. 0 Hello everyone, I am using scVI to correct batch effects. However, I have encountered a problem and I need help from all of you. My layout for my data: adata AnnData object with n_obs × n_vars = 33486 × 352365 obs: ‘features’, ‘_scvi_batch’, ‘_scvi_labels’ var:…

How to fix attributeError: module ‘scvi’ has no attribute ‘model’? 0 Hi all, I try to follow the tutorial below and get an error. 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 in my case: github.com/scverse/scvi-tools/issues/824 scvi.model.SCVI.setup_anndata(adata) vae = scvi.model.SCVI(adata) vae.train() ————————————————————————— AttributeError Traceback (most recent…

SCVI problem 0 Good morning, I am trying to use SCVI-tool to integrate my data, however, I meet a problem. I hope you guys could help me out. I meet the error message- “module ‘scvi’ has no attribute ‘data’ when I run scvi.model.SCVI.setup_anndata(adata) command. My SCVI – tool version is…

Here is the error message from before ValueError Traceback (most recent call last) <ipython-input-29-3de112adfeee> in <module> —-> 1 vae5.train() /opt/conda/lib/python3.8/site-packages/scvi/model/_totalvi.py in train(self, max_epochs, lr, use_gpu, train_size, validation_size, batch_size, early_stopping, check_val_every_n_epoch, reduce_lr_on_plateau, n_steps_kl_warmup, n_epochs_kl_warmup, adversarial_classifier, plan_kwargs, **kwargs) 257 **kwargs, 258 ) –> 259 return runner() 260 261 @torch.no_grad() /opt/conda/lib/python3.8/site-packages/scvi/train/_trainrunner.py in __call__(self)…

DOI: 10.18129/B9.bioc.scviR   This is the development version of scviR; to use it, please install the devel version of Bioconductor. experimental inferface from R to scvi-tools Bioconductor version: Development (3.17) This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another…

Hi I have spent a few days to learn how totalvi analyze CITE-seq data and I am bit confused by the contrasting steps between Scanpy and totalvi: I have used Scanpy for 10x scRNA-seq for over 2 years now and I love it.The typical steps are as follows: Read in…

cwang February 21, 2023, 12:04am 1 Hi, I’m trying to learning analysis by following various tutorials and when using scvi to predict doublets, my kernel keeps dying. This is the code that I’m trying to run scvi.model.SCVI.setup_anndata(adata) vae = scvi.model.SCVI(adata) vae.train() There was post about this same issue and two…

data.pbmc_seurat_v4_cite_seq Dataset of PBMCs measured with CITE-seq (161764 cells). data.spleen_lymph_cite_seq Immune cells from the murine spleen and lymph nodes [GayosoSteier21]. data.heart_cell_atlas_subsampled Combined single cell and single nuclei RNA-Seq data of 485K cardiac cells with annotations. data.pbmcs_10x_cite_seq Filtered PBMCs from 10x Genomics profiled with RNA and protein. data.purified_pbmc_dataset Purified PBMC dataset…

WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data 0 I want to build a UMAP from CITE-seq data with a joint embedding of the scRNA-seq and protein ab data. What’s the ‘best’ method in terms of representing the most accurate embedding? In the totalVI paper, they say totalVI >…