Similar posts • Search »

• Seurat Clustering - Cluster Numbers from 1 instead of 0
  Hi All, I am analysing Single-cell RNAseq data with Seurat. When I cluster my samples using "Fin...
• using distinct versions of SEURAT on a SLURM cluster
  Dear all, 'd appreciate having your suggestions on the following please : I am running scRNA-seq...
• Performing integration analysis of two datasets of different sizes in Seurat
  I am following the Satija Lab's ctrl vs stim Seurat tutorial (https://satijalab.org/seurat/v3.1/i...
• (Single-cell RNA seq; R - Seurat) Re-clustering after removing cells using SubsetData
  I have a question regarding **re-clustering after removing cells using SubsetData** (R - Seurat p...
• pulling out TCR data
  Hello! I have successfully loaded my VDJ data into my seurate object. Once I have identified the ...
• scRNAseq Seurat conserved markers among clusters
  Hello, I am trying to find the most highly expressed genes that are conserved in all my scRNAseq ...
• How to record Seurat DE analysis efficiently?
  So Seurat can generate ViolinPlots that illustrate differential gene expression across clusters. ...
• cellRanger 2.0 to Seurat 3.1.2
  Hi, anybody know if data from cellRanger 2.0 are still readable with Seurat 3.1.2? I am getting a...
• Skipping Clustering in Seurat
  Hello, I was wondering if there is a possibility to skip the clustering step in Seurat and just ...
• Seurat to Dataframe with ONLY counts, cells, and cluster labels?
  I'm trying to run MDSeq, which appears to require a plain old data frame - counts and cells, and ...
• Calculating in SEURAT, list of highly dysregulated genes across conditions in a particular cluster.
  I am trying to integrate two datasets from different conditions using Seurat vignette "Integratin...
• Setting Contrast for DESeq2 results
  I need to compare both Ly49+ versus Ly49− and MOG versus MOG plus SP. Column data in at the botto...
• PCA vs ICA prior to t-SNE or UMAP
  I'm working on a project involving analyzing scRNA-seq data. A large part of the project involves...
• SEURAT scRNA-seq and library contribution for each cluster
  Hello Everyone, I'm analyzing three replicates samples with Seurat pipeline and I made clusters ...
• Differential expression analysis in Seurat
  Hi, I would like to get some clarification on whether I should be using the RNA assay or the SCT...
• determine the robustness of single-cell clusters
  Hi All, I'm working on single-cell RNA seq data mostly with the Seurat package. I need to assess...
• DEG analysis between control and treatment groups in integrated scRNAseq analysis
  I am using the Seurat platform to perform integrated analysis on my single cell data. I have fou...
• Seurat FindMarkers avg_logFC for integrated dataset
  Hi, I am having trouble understanding the avg_logFC results of an integrated dataset (control an...
• Gene set enrichment analysis using a curated gene list and cluster DE genes
  I have a curated gene list using which I would like to carry out enrichment analysis on DE genes ...
• Single cell DEG analysis. Wildly different results from different FindMarkers test
  Hello and thank you in advance for your help. I am doing a single cell RNA seq experiment and a...
• A brief question regarding regressing out cell cycle effects or ribosomal/mitochondrial genes
  Im using the Seurat platform on some data but I think the question applies regardless of platform...
• Single Cell RNAseq Imputation in Seurat
  Hi, I was writing to find out if anyone has experience doing imputation in Seurat. Where in the...
• Subsetting fastMNN integrated Object
  Hello, I have integrated multiple datasets successfully using fastMNN. I am now needing to subse...