Скачать с ютуб Automatic cell-annotation for single-cell RNA-Seq data: A detailed SingleR tutorial (PART 1) в хорошем качестве

Automatic cell-annotation for single-cell RNA-Seq data: A detailed SingleR tutorial (PART 1)

One of the most challenging task in processing single-cell RNA-Seq data is to annotate cell types. In this video I walk through what is a typical cell annotation workflow, discuss various annotation strategies and their strengths and pitfalls. Further, I explain how #SingleR works and demonstrate how to annotate cell types using SingleR using a single reference dataset. Lastly, I discuss various diagnostics to evaluate cell type assignments by singleR and visualize cell labels as a UMAP. I hope you find this video helpful! Leave your thoughts in the comment section below! ▸ Link to Data: https://www.10xgenomics.com/resources... ▸ Link to Code: https://github.com/kpatel427/YouTubeT... ▸ Resources/Vignettes: 1. https://www.nature.com/articles/s4159... 2. http://bioconductor.org/books/release... 3. http://bioconductor.org/books/3.14/OS... Chapters: 0:00 Intro 0:51 Overview of cell annotation workflow 2:45 Strategies for automatic cell annotation 4:06 Marker-based annotation approach 5:41 Reference-based annotation approach 7:05 How does SingleR work? 9:30 Study design and goal of the analysis 10:09 Data used for demonstration 10:27 Reading data, filtering and pre-processing in Seurat 15:41 Pointers to choose reference dataset to run SingleR 18:11 Fetching reference data from celldex package 20:20 Run SingleR() 22:04 Understanding singleR output 23:04 Visualize singleR labels in a UMAP plot 25:03 Annotation diagnostic 1: Based on scores within cells 28:02 Annotation diagnostic 2: Based on deltas across cells 29:13 Annotation diagnostic 3: Comparing cell type assignments to unsupervised clustering You can show your support and encouragement by buying me a coffee: https://www.buymeacoffee.com/bioinfor... To get in touch: Website: https://bioinformagician.org/ Github: https://github.com/kpatel427 Email: [email protected] #bioinformagician #bioinformatics #singleR #singlecell #annotationdbi #reversestranded #directstranded #strandedness #survival #survminer #survivalanalysis #kaplanmeier #tcga #gdcportal #tcgaportal #nci #cran #bioconductor #funcotator #variantcalling #variants #gatk #vcf #gvcf #haplotype #alleles #geneticvariants #mutations #gff3 #gff #gtf #sam #bam #phred #fasta #fastq #singlecell #10X #ensembl #biomart #annotationdbi #annotables #affymetrix #microarray #affy #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #GEO #rnaseq #ngs