Welcome to our step-by-step tutorial on analyzing single-cell RNA sequencing (scRNA-seq) data using the PBMC dataset from 10x Genomics and the CompuFlair pipeline! In this video, we'll walk you through the entire process, from accessing and downloading the dataset to performing in-depth analysis and visualization using R Studio.
*What You'll Learn:*
1. *Accessing and Downloading Data:*
- Navigate the 10x Genomics website to find and select the PBMC dataset.
- Fill out the necessary form to download the filtered matrix or HDF5 file.
2. *Preparing the Data:*
- Decompress the downloaded file.
- Explore the decompressed files: barcode, gene, and matrix files needed for analysis.
3. *Finding the Right Pipeline:*
- Use CompuFlair’s search engine to find the most relevant analysis pipeline.
- Read descriptions, check citations, and select the best pipeline for your analysis.
4. *Setting Up the Analysis Environment:*
- Use R Studio for executing the provided R codes.
- Import and compress the data for faster upload and smoother processing.
5. *Executing and Understanding the Code:*
- Copy and run tailored code blocks in R Studio.
- Learn how to modify paths and parameters for your specific dataset.
- Visualize and interpret plots, such as quality control metrics and principal component analysis.
6. *Quality Control and Data Filtering:*
- Visualize and filter mitochondrial gene percentages.
- Find and scale highly variable genes.
- Perform dimensionality reduction using PCA and UMAP.
7. *Clustering and Marker Gene Analysis:*
- Identify and visualize cell clusters.
- Find differentially expressed genes and potential marker genes.
- Annotate clusters using canonical genes.
8. *Saving and Exporting Results:*
- Save important data objects and figures.
- Download results to your local disk for further analysis.
*Follow Along with Code and Tips:*
- We provide detailed explanations for each code block.
- Get tips on parameter selection and handling errors.
- Learn how to explore additional genes in your dataset.
*Why Watch This Tutorial?*
- Ideal for beginners and intermediate users in the field of single-cell RNA-seq analysis.
- Comprehensive and easy-to-follow steps.
- Practical tips and troubleshooting advice.
- Utilize powerful tools like 10x Genomics and CompuFlair for cutting-edge analysis.
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*#SingleCellRNASeq #Bioinformatics #10xGenomics #CompuFlair #RStudio #scRNAseqAnalysis #DataScience*
Thank you for watching, and happy analyzing!
*CompuFlair URL:*
www.compu-flair.com
16 июн 2024
