Tag: SingleR

In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…

Dear all, I have the following issue: I have a Seurat object with 7 layers of raw gene expression counts for 7 different patients. In order to annotate the object with SingleR I have now used the function “JoinLayers” to combine all counts into one layer of counts of all…

Good afternoon, I am working with a dataset of 7 patients. I have merged all raw counts to one count object with JoinLayers: Now I would like to know whether there are certain genes differentially expressed between my Seurat clusters. For that I ran markers_all<-FindAllMarkers(kid.filtered_new, test.use=”DESeq2″, slot=”counts”) However, it does…

Options for assigning cell labels to barcodes from CITE-seq experiment 0 I have barcodes from a CITE-seq experiment that I would like to assign cell labels to. To accomplish this task, I used the Monaco reference database as input into SingleR based on the RNA expression data. I would now…

DOI: 10.18129/B9.bioc.DelayedArray     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see DelayedArray. A unified framework for working transparently with on-disk and in-memory array-like datasets Bioconductor version: 3.11 Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to…

Overlapping cluster/annotation 1 Dear Senior Fellows, I used Seurat to cluster my single cells and use singleR for annotation, but there seems to be an overlapping cluster / annotation. Are they doublets? or just error with annotation (circle in red). if they are doublets, is there any standard workflow in…

How to get top 10 genes expressed in a cluster ( for cell type identification)? 0 Hi all, I try to label clusters but singleR result is not consistent with the marker gene for a cell type. Findmarker() or Findallmarker() seems could not get genes express in a cluster but…

Use of plotDeltaDistribution() to assess the quality of automatic annotation of scRNA seq data 0 Hello, I attempted to use the SingleR function to automatically find out the cell types of each scRNA seq clusters. After that, I use the plotDeltaDistribution() function to assess the quality of automatic annotation. From…

automatic clustering annotation using python 0 Hello, I’m currently working on single-cell data processing using scanpy. After determining the clusters, the next step is cluster annotation. My question is: Is there a Python tool that allows for automatic cluster annotation, similar to SingleR in R? I’m specifically looking for a…

annotating single-cell cluster from Drosophila melanogaster using SingleR? 0 We have a data set from Drosophila melanogaster, we don’t know much about. We ran the Seurat-workflow and got various clusters. I would like to try and annotate this clusters in an automated manner. I know the SingleR package is the…

How to plot combined bar graph in R 1 After running the following function count_table <- table(Sample.@meta.data$seurat_clusters, Sample@meta.data$orig.ident, Sample@meta.data$singlr_labels) View(count_table) str(count_table) ‘table’ int [1:15, 1:2, 1:20] 0 0 0 0 0 0 2 0 273 0 … – attr(*, “dimnames”)=List of 3 ..$ : chr [1:15] “0” “1” “2” “3”…

Cell clusters in ZIKV-infected mouse testis defined by scRNA-Seq To investigate the influence of ZIKV infection on testes, testicular cells from ZIKV-infected (14 dpi.) and uninfected A6 male mice (Ifnar−/− mice) were analyzed by single-cell RNA sequencing (scRNA-Seq). After filtering out poor-quality cells, 11014 cells in control testes and 11974…

DOI: 10.18129/B9.bioc.scRNAseq   This is the development version of scRNAseq; for the stable release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: Development (3.17) Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso [aut, cph],…

scRNAseq package and cell type annotations 1 @0dc78e90 Last seen 4 hours ago Australia I would like to annotate or label UMAP clusters with cell types in a multiple myeloma single-cell RNA-seq dataset using the scRNAseq R package in conjunction with the SingleR package, if possible. I found a dataset…

If using singeR return more clusters than available ones should I do reclustering? 1 Hi all, I did use a reference dataset to do automated annotation of my dataset. I do have roughly 20 clusters. But running singleR it annotated my dataset with more sub clusters. I was wondering should…

Question about scRNA-seq cell annotation using SingleR 0 Hi guys, This is my first time analyzing a scRNA-seq dataset, and now I’m a bit stuck at the cell annotation step with SingleR. My dataset is from an enriched population from PBMC, and I’m mostly interested in different types of blood…

Batch effect correction methods (Seurat v3, Harmony, fastMNN, Liger) 0 I applied different batch effect correction methods including Seurat v3 integration, Harmony, fastMNN, and Liger on 52 single-cell RNA PBMC samples from different 4 public datasets. The results from the methods presented in the figure (samples grouped by sample_ID, datasets,…

This blog post was co-written by the Bioconductor Community Manager, Maria Doyle, and the lead developer of CuratedAtlasQueryR, Stefano Mangiola. We are excited to announce the launch of the CuratedAtlasQueryR package! Millions of cells are now at your fingertips as the harmonized and reannotated CELLxGENE single-cell human atlas can be…

singleR annotation shows overlapping clusters 0 Hello everyone, I used singleR to annotate my clustered Seurat dataset. Before annotating using singleR I did manual annotation using marker genes. Below is the result of my manual annotation Then, I used singleR and below is the annotation results. The result shows that…

What should I do if the gene IDs in my reference dataset and test dataset are different 1 Hi everyone, I am trying to annotate my single cell dataset (integrated dataset) using singleR. However, I am getting the error “no common genes between ‘test’ and ‘ref’”. I realized that the…

met a problem while installing the LTLA/SingleR 1.5.3, urgent, thank you very much for help installing to /home/binf0xx/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-SingleR/00new/SingleR/libs ** R ** inst ** byte-compile and prepare package for lazy loading Error: object ‘I’ is not exported by ‘namespace:S4Vectors’ Execution halted ERROR: lazy loading failed for package ‘SingleR’ removing ‘/home/binf0xx/R/x86_64-pc-linux-gnu-library/4.0/SingleR’ Read…

How to use “SingleR” on the marker genes from `FindAllMarkers` for each cluster? 0 Hi, I tried to use SingleR to identify cell types for clusters. I have the table of results from FindAllMakers of Seurat package. I know that I can use: SingleR(GetAssayData(seurat.object, assay = assay, slot = “data”),…

Can SingleR be reused to identify cell types after subsetting the original Seurat Object 0 Hi, I got a Seurat object and applied SingleR to identify cell types. Then subset the epithelial cell then redid the clustering on this cell type only. So now I got some new clusters. My…

DOI: 10.18129/B9.bioc.scRNAseq     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: 3.11 Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso…

  Mostly because it’s typically unnecessary given that reference-based classification should yield a similar result without being subjected to potential biases introduced during the integration process. SingleR (and presumably Seurat, I don’t know as I don’t use it) uses a reference dataset and asks “Which reference sample’s expression profile is…