Unexplainable missing values in single cell Seurat object

Unexplainable missing values in single cell Seurat object - Biostars

Did you filter your data matrix outside of Seurat or did you set some values to NA? · Is the feature present in your count matrix even?

Issue with Missing Dimnames and Assay Class Change in Seurat v5 ...

You'd basically be reintroducing the same dimnames you have in the counts matrix back to the lost Dimnames layer in your Seurat Object. However, the resulting ...

Single cell seurat cluster missing after integration with ... - GitHub

I followed the tutorial vignette to perform integration of spatial seurat object with single-cell RNAseq data. However I noticed certain seurat ...

missing value recovery for single cell RNA sequencing data - PubMed

The advent of single-cell RNA sequencing (scRNA-seq) technology has revolutionized our ability to explore cellular diversity and unravel the ...

SCTransform | Illumina Connected Software

Impute missing values ... We recommend performing the normalization on a single cell raw count data node. ... Seurat object. It is used for downstream ...

DittoDimPlot errror: Cannot find 'NA' in this Seurat object

I am using seurat to analyze spatial data. I have 8 datasets from 2 batches merged together. I aim to use dittoSeq for visualizations, however, I am facing a ...

Bioinformatics Answers - Biostars

Comment: Unexplainable missing values in single cell Seurat object by Gerard ▴ 10. raw_counts <- seurat_object@assays$RNA@features["geneofinterest", , drop ...

The Sum of Two Halves May Be Different from the - ProQuest

... missing data [18]. For the latter, the assessment ... single-cell mRNA data and bulk ChIPseq data. For ... Seurat objects [56] were created ...

Release Notes | Illumina Connected Software

Import single cell data · Importing 10x Genomics ... Impute missing values · Normalization · Normalize to ... Added support to import Seurat 5 object. Added ...

Deconvolution of Bulk Gene Expression Profiles with Single-Cell ...

... Seurat (Stuart et al., 2019). (version 3.2.0) R package. First, the single-cell GEPs of AML patients were integrated and imported into a Seurat object. All.

4 Data Wrangling scRNAseq | ANALYSIS OF SINGLE CELL RNA ...

seurat@assays$RNA@counts is a slot that stores the original gene count matrix. We can view the first 10 rows (genes) and the first 10 columns (cells). seurat@ ...

ASBMR Annual Meeting Abstract Supplement 2021 - AUB

... cell-rich region, with regenerative abilities in ... single-cell transcriptomic analysis (scRNA-seq) ... values. At baseline, PTH was. 3.4+/-4.5 pg/mL ...

Abstract book BioSB 2022.docx

overcome the high sparsity of single-cell data, we use cell ... that only a single objective would lead to the highest synthesis of biomass of both cell types.

Seurat - Guided Clustering Tutorial - Satija Lab

The object serves as a container that contains both data (like the count matrix) and analysis (like PCA, or clustering results) for a single- ...

Gene Expression Data Analysis; A Statistical and Machine Learning ...

Most techniques estimate the missing values for a given object based ... GRN analysis, single-cell ... values occur randomly, one can remove the instances with ...

Why do authors never attach their Single Cell analysis structure to ...

It is annoying having to update the seurat object going through several versions now. Especially now with seurat v5 there was a bug where ...

Seurat v5 Command Cheat Sheet - Satija Lab

... data using Seurat v5. ... Access cell names and metadata. Get cell names. Since Seurat v5 object doesn't require all assays have the same cells ...

Methods and Protocols

nonlinear SC from bulk and single-cell RNA-seq data of pure cell ... tion on the full Seurat object ... One limitation of scRNA-seq is that missing data does not.