• How to merge multiple single cell sequencing data after processing by CellRanger software

    Hi everyone, I have some questions about single cell RNA-seq analysis.
    I just got the output dat...

  • Using dropEst output for Seurat

    Hello All,

    I have obtained some scRNAseq data from a repository and the data are in count.matric...

  • How to delete Assay from Seurat object?

    If I have a seurat object with two assay classes "ADT" and "RNA" how do I remove one or the other...

  • Seurat heatmap across conditions

    Hello,

    I have a seurat object that has 3 conditions merged. When plotting feature plots I can s...

  • Merging Seurat objects together and gene alignment

    Hi all, I was wondering if somebody could help with a question i have regarding the seurat pipeli...

  • Two different library preps

    Hello I have to combine two data sets from 10x in seurat. one data set was prepared following 5' ...

  • How to use monocle to import a loom file?

    I want to merge my seurat data of 3 experimental time points with the Hippocampus data provided ...

  • Analyzing TCR clonotype in Seurat

    Hello, I have merged my VDJ data into my Seurat object by adding it as metadata. Now is there a w...

  • Seurat - weird behavior in the counts object.

    So I've been trying to learn some Seurat recently and while working on some data I noticed that t...

  • plotting two genes in Seurat ScRNAseq

    I have a clarification about about using Seurat package (link is satijalab.org/seurat/pbm...

  • Associating VDJ clonotyping data with scRNA-seq in Seurat

    Single cell technologies are booming, but figuring out how to integrate multimodal data sets is c...

  • How to concurrently filter RNA and CITEseq data within seurat object

    I have a Seurat object I created from RNA and CITEseq data. I load the matrices and create a seur...

  • single cell ATAC-seq cicero gene activities in Seurat

    Hi everyone!

    I am loading my single-cell ATACseq data using cicero, and then I create gene activ...

  • How many PCs should be considered for downstream analyses?

    Hi All,

    I have two groups WT and KO.

    As per the Jackstraw plot, ‘Significant’ PCs will show a s...

  • Re-arrange conditions in Seurat

    Hello,

    Would anyone know how to re-arrange the output of featureplots/dimplots when using the '...

  • Color code samples

    Hello, I have a merged seurat object with 3 different samples in it. How would I do about color c...

  • Does having sample identifiers in a Seurat object semi-supervise PCA results?

    I'm working with 4 samples (10x sequenced) and loading them into Seurat using the Read10x() funct...

  • Seurat DefaultAssay integrated vs RNA

    Hi,

    Whats the difference between the following in Seurat objects?

    DefaultAssay(combined.dat...

  • Seurat: can someone explain how to identify cell types in clusters

    I'm confused on Seurat's tutorial of integrating two datasets.

    Seurat has this: nk.markers &lt...



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