Tag: SCVI

Vae_q.latent_space_classifer_ not found in totalVI CITE-seq reference mapping tutorial – scvi-tools

We are following the tutorial located here to create a reference and map cell idents to a query. CITE-seq reference mapping with totalVI — scvi-tools In “Query cell type prediction”, we receive an error that vae_q does not have latent_space_classifier_, when running: predictions = vae_q.latent_space_classifer_.predict(query.obsm[“X_totalvi_scarches”]) Should this be vae instead…

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bam file missing barcode and UMI info

Hi, I used STARsolo but my bam files, below, are missing barcode and UMI info: (/scratch/work/malonzm1/.conda_envs/scvi-env) [malonzm1@login3]/scratch/cs/pan-autoimmune/data/star/scRNAseq/GSE151177/SRR11848679% samtools view SRR11848679Aligned.out.bam|head -n5 NB500961:910:HJ5TWBGXC:1:23304:10007:9225 0 chr1 6100902 255 55M * 0 0 TTCGGAGCCCCCACTGTTTCCCACTCAGCTTTGTGCTCAGATCCCAGGTCCCAAG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE NH:i:1 HI:i:1 AS:i:54 nM:i:0 NM:i:0 MD:Z:55 jM:B:c,-1 jI:B:i,-1 NB500961:910:HJ5TWBGXC:1:13111:23716:1741 0 chr1 6100902 255 4S51M * 0 0 GAGATTCGGAGCCCACACTGTTTCCCACTCAGCTTTGTGCTAATATCCAAGGTCC…

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Transfer harmony-integrated scRNA-seq data to scanpy

Transfer harmony-integrated scRNA-seq data to scanpy 1 I have integrated two scRNA-seq datasets using harmony method. Unlike Seurat integration, Harmony just adds extra embeddings for further clustering and other analysis. However, the data (raw counts, normalized, and scaled slots) is the same as in unintegrated data. So, when I transfer…

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scanpy problem for empty cells

Hello everyone, I encountered a problem when I use scanpy analysis my data. When I tried to remove scrublet, and then I encountered following error: filtered out 42144305 cells that have less than 200 genes expressed Running Scrublet normalizing counts per cell /rsrch4/home/canbio/conda/envs/scvi-env/lib/python3.11/site-packages/scanpy/preprocessing/_normalization.py:197: UserWarning: Some cells have zero counts warn(UserWarning(‘Some…

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Help with scvi error

Help with scvi error 0 Hi all, I could not find this error after searching, would you please have a suggestion? I paste the line that show the error message to make the post not too long. I appreciate it! sc.pp.neighbors(adata, use_rep = ‘X_scVI’) sc.tl.umap(adata) sc.tl.leiden(adata, resolution = 0.5) RuntimeError…

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Zafrens, Inc. Single-cell Bioinformatics Scientist in San Diego, CA | 865232727

Zafrens, Inc., a cutting-edge biotechnology company that is trying to redefine lifesciences product development, is seeking a Single-cell Bioinformatics Scientist. This is a great opportunity for someone with a passion for bioinformatics and an interest in innovative product development to work with a team of creative and adventurous scientists who…

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Can I using scVI to integrate data, then using R to conduct following analysis?

Can I using scVI to integrate data, then using R to conduct following analysis? 2 Hello everyone, I am wondering if I could use Python to integrate my data and then use R to conduct downstream analysis, such as CellChat, etc. Thank you,Andy R python single-cell • 30 views •…

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How to install solo-sc or use hashsolo from scvi? – scvi-tools

When I attempt to install solo in conda environment lately, I have been encountering the following error. pip install solo-sc Collecting solo-sc Using cached solo-sc-1.3.tar.gz (18 kB) Preparing metadata (setup.py) … done Collecting ConfigArgParse (from solo-sc) Obtaining dependency information for ConfigArgParse from files.pythonhosted.org/packages/6f/b3/b4ac838711fd74a2b4e6f746703cf9dd2cf5462d17dac07e349234e21b97/ConfigArgParse-1.7-py3-none-any.whl.metadata Using cached ConfigArgParse-1.7-py3-none-any.whl.metadata (23 kB) Collecting pandas…

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Integration more than one million cell

Integration more than one million cell 1 Hello everyone, I have encountered a dataset with over one million cells, and I have tried using scVI, scANVI, and scanorama for integration. Unfortunately, these methods did not perform as well as I had hoped. Therefore, I would like to kindly ask if…

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Loading an scVI model from a pytorch lightning checkpoint – scvi-tools

I want to be able to evaluate the scvi model every n epochs on a benchmark. Therefore, I am trying to save the model every n epochs and loading it again in order to run the benchmark on each saved model. The only way I have found to save the…

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how to determine n_cells_by_count

Hello, I followed this toturial (github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb ) in order to preceed single cell rna seq analysis using scanpy. for the first step data filtring I applied this script def pp(csv_path): adata = sc.read_csv(csv_path).T sc.pp.highly_variable_genes(adata, n_top_genes = 2000, subset = True, flavor=”seurat_v3″) scvi.model.SCVI.setup_anndata(adata) vae = scvi.model.SCVI(adata) vae.train() solo = scvi.external.SOLO.from_scvi_model(vae) solo.train()…

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Single-cell Bioinformatics Scientist job with Zafrens, Inc.

Zafrens, Inc., a cutting-edge biotechnology company that is trying to redefine lifesciences product development, is seeking a Single-cell Bioinformatics Scientist. This is a great opportunity for someone with a passion for bioinformatics and an interest in innovative product development to work with a team of creative and adventurous scientists who…

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Debugging Issue for CITE-seq analysis with totalVI juytper notebook tutorial – scvi-tools

Bakar June 13, 2023, 8:50pm 1 I am having issues addressing a error when trying to go through the CITE-seq analysis with totalVI notebook on my personal computer. An error surfaces when I try to run the following cell block: ————————————————————————— AttributeError Traceback (most recent call last) Cell In[9], line…

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scRNA seq integration

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…

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Scanpy and SCVI help.

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:…

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module ‘scvi’ has no attribute ‘model’?

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…

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SCVI problem

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…

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Running TOTALVI data in which subset of cells do not have citeseq data – scvi-tools

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)…

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Bioconductor – scviR (development version)

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…

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Comparing steps of Scanpy for scRNQ-seq and totalvi for CITE-seq – scvi-tools

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…

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Kernel dying when using scvi to train a model (m1 mac) – scvi-tools

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…

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Datasets – scvi-tools

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…

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WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data

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 >…

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