Tag: InferCNV

Working with infercnv results for large datasets 0 I’m currently working with infercnv on a large dataset of 10x scRNA. I want to meaningfully visualise the results but with the resulting matrix of cnv results being so large it becomes prohibitive to visualise even with rasterisation. I was wondering if…

How to distinguish between normal and malignant epithelial cells based on CNV? 1 One of the method that is used to find malignant cells in tumor scRNA-seq data is infercnv. This, this, and this papers used infercnv outputs to find cancer cells among other epithelial cells. They separate cancer and…

InferCNV results interpretation 0 I’d been looking for a way to distinguish cancer cells from other epithelial cells in tumor scRNA-seq data and found inferCNV method. It finds cells with large-scale chromosomal deletions or insertions from scRNA-seq data based on “normal” cell references. I followed their test running on pediatric…

I’m working with matched single cell data, where we have treated and untreated samples for the same patient. I ran CNV analysis using the infercnv package. I’ve followed the tutorial: # data matrix counts_matrix <- scData@assays$RNA@counts meta = data.frame(labels = Idents(scData), row.names = names(Idents(scData))) unique(meta$labels) # check the cell labels…

Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS  PubMed  PubMed Central  Google Scholar  Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS  PubMed  PubMed Central  Google Scholar  Yokoyama, A….

Strategy for stripping human sequence data of genetic information To lower the barriers in sharing sequence data, we propose, like others recently17, to remove information on genetic variation that could be used to infer the identity from aligned reads and compromises the privacy of the donor (Fig. 1a). Genetic variation, including…

InferCNV how to choose the right reference? 1 Hello everyone! Could you help me to choose the correct reference for scRNA data if I need to identify CNVs among the malignant clusters that are represented as immune cells with an epithelial phenotype (CTC). What is more correct to take healthy…