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  • Getting Started with Seurat • Seurat - Satija Lab

    satijalab.org

    https://satijalab.org/seurat/articles/get_started.html

    WebGetting Started with Seurat v4. Source: vignettes/get_started.Rmd. We provide a series of vignettes, tutorials, and analysis walkthroughs to help users get started with Seurat. You can also check out our Reference page which contains a full list of functions available to users.

    DA: 91 PA: 82 MOZ Rank: 49

  • Seurat - Guided Clustering Tutorial • Seurat - Satija Lab

    satijalab.org

    https://satijalab.org/seurat/articles/pbmc3k_tutorial.html

    WebOct 31, 2023 · Seurat - Guided Clustering Tutorial • Seurat. Compiled: October 31, 2023. Source: vignettes/pbmc3k_tutorial.Rmd. Setup the Seurat Object. For this tutorial, we will be analyzing the a dataset of Peripheral Blood Mononuclear Cells (PBMC) freely available from 10X Genomics. There are 2,700 single cells that were sequenced on the Illumina NextSeq …

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  • Getting Started with Seurat • Seurat

    satijalab.org

    https://satijalab.org/seurat/articles/get_started_v5_new

    WebWe provide a series of vignettes, tutorials, and analysis walkthroughs to help users get started with Seurat. You can also check out our Reference page which contains a full list of functions available to users.

    DA: 43 PA: 22 MOZ Rank: 89

  • Getting started with Seurat

    github.io

    https://davetang.github.io/muse/seurat.html

    WebApr 15, 2024 · The tutorial states that “The number of genes and UMIs (nGene and nUMI) are automatically calculated for every object by Seurat.”. The nUMI is calculated as num.mol <- colSums(object.raw.data) , i.e. each transcript is a unique molecule. The number of genes is simply the tally of genes with at least 1 transcript; num.genes <- colSums(object ...

    DA: 32 PA: 31 MOZ Rank: 43

  • Introduction to single-cell RNA-seq analysis using Seurat

    github.io

    https://melbintgen.github.io/Intro-to-scRNA-seq-analysis/scRNAseq_workshop.html

    WebFeb 28, 2024 · Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to …

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  • Seurat Guided Clustering Tutorial - Danh Truong, PhD

    danhdtruong.com

    https://danhdtruong.com/Seurat-Guided-Clustering-Tutorial/

    WebJul 2, 2020 · Seurat Guided Clustering Tutorial. 26 minute read. While the vignette on the Seurat website already provides good instructions, I will be using this to give additional thoughts and details that could help beginners to Seurat. In addition, I will provide some recommendations on the workflow as well. Loading the files.

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  • 8 Single cell RNA-seq analysis using Seurat

    singlecellcourse.org

    https://www.singlecellcourse.org/single-cell-rna-seq-analysis-using-seurat.html

    WebLet’s now load all the libraries that will be needed for the tutorial. library(Seurat) library(ggplot2) library(SingleR) library(dplyr) library(celldex) library(RColorBrewer) library(SingleCellExperiment) 8.1 Basic quality control and filtering.

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  • Chapter 3 Analysis Using Seurat | Fundamentals of scRNASeq …

    github.io

    https://holab-hku.github.io/Fundamental-scRNA/downstream.html

    WebIn this tutorial, we will learn how to Read 10X sequencing data and change it into a seurat object, QC and selecting cells for further analysis, Normalizing the data, Identification of highly variable features (feature selection), Scaling the data, Perform linear dimensional reduction and Visualization.

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  • GitHub - satijalab/seurat: R toolkit for single cell genomics

    github.com

    https://github.com/satijalab/seurat

    WebThis updates introduces new functionality for spatial, multimodal, and scalable single-cell analysis. Seurat v5 is backwards-compatible with previous versions, so that users will continue to be able to re-run existing workflows. Instructions, documentation, and tutorials can be found at: https://satijalab.org/seurat.

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  • Getting started with Seurat - Dave Tang's blog

    davetang.org

    https://davetang.org/muse/2017/08/01/getting-started-seurat/

    WebAug 1, 2017 · Getting started with Seurat. single cell Davo August 1, 2017 30. This post is outdated; please refer to the official Seurat vignettes for more information. This post follows the Peripheral Blood Mononuclear Cells (PBMCs) tutorial for 2,700 single cells. It was written while I was going through the tutorial and contains my notes.

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