Tag: CITEseq

Help concatenating var for cite seq – scanpy

I have a CITE seq experiment where the GEX and antibody capture were mapped separately, so that I have to load in two different matrices. adata_adt = sc.read_10x_mtx( “data/CITESeq_381/”, gex_only = False ) adata_gex = sc.read_10x_mtx( “data/GEX_381/filtered_feature_bc_matrix/”, gex_only = True ) I subset to only cells with GEX and ADT…

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single cell multi-modal data (CITEseq) batch correction

single cell multi-modal data (CITEseq) batch correction 0 I’m working with a BD Rhabsody AbSeq data set containting a targeted scRNA and surfce protein (ADT) layer measured in two batches. In general I aim to integrate both modalities (e.g. MOFA+ or SeuratV4) for a joined analysis. While I perform QC…

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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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using CITE-seq data to cluster single cells

using CITE-seq data to cluster single cells 0 Hello, I am trying to cluster single cells using the ADT reads from the CITEseq (generated with the 10x platform). Ideally, I would like to use the information from two ADT features. I have tried the kmeans function on a count matrix…

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Cell Type Prediction – covering 45 immune cell types

Tool:Cell Type Prediction – covering 45 immune cell types 0 Dear Colleagues, We just released a new tool for predicting cell types from single-cell RNA-seq data (and scRNA-seq + CITE-Seq). Currently, it covers 45 sub-types of immune cells. More subtypes are continuously being added. This tool is available in both…

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Corelate TCR data to clusters/GEX/CITEseq data

Corelate TCR data to clusters/GEX/CITEseq data 1 Hello everyone, I just added my TCR VDJ data as metadata to my Seurat object (as described in the tutorial here). So, I basically ended up with two different collumns of metadata where my barcodes are assigned to the clonotypes and the cdr3…

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