Comprehensive Guide to Downstream Analysis for Single-Cell ATAC-Seq in R | scATAC-Seq Workflow
A detailed walk-through of downstream analysis steps to annotate single-cell ATAC-Seq data by integrating with single-cell RNA-Seq dataset, to perform differential accessibility analysis and visualize genomic regions of interest. In this demonstration, we continue with our pre-processed single-cell ATAC sequencing dataset from 10X Genomics in R using the #Signac package. I hope you liked the video. I look forward to your comments under the comments section!
▸ Link to Data:
Pre-processed scRNA-Seq data: https://signac-objects.s3.amazonaws.c...
▸ How to pre-process scATAC-Seq data (Part 1 of this video):
• How to analyze single-cell ATAC-Seq d...
▸ Link to Vignette:
https://stuartlab.org/signac/articles...
▸ Link to code:
https://github.com/kpatel427/YouTubeT...
▸ Other Useful Resources:
1. Strategies to annotate scATAC-Seq data: https://cdn.10xgenomics.com/image/upl...
2. How to pre-process scRNA-Seq? • How to analyze single-cell RNA-Seq da...
3. Find markers and cluster identification in single-cell RNA-Seq using Seurat: • Find markers and cluster identificati...
4. Single-cell playlist: • Tutorial: Single-cell
Chapters:
0:00 Intro
0:44 scATAC-Seq Analysis Workflow
1:52 Strategies to annotate scATAC-Seq cells
4:30 Dataset and requirements for demonstration
6:06 Starting with pre-processed scATAC-Seq
6:30 What is a gene activity matrix?
8:29 Creating a gene activity matrix
10:52 Visualizing gene activity of canonical markers
13:38 Visualizing cell annotations in scRNA-Seq
17:02 Integrating scATAC-Seq with scRNA-Seq
17:58 Transfer labels from scRNA-Seq to scATAC-Seq
19:54 Visualizing scATAC-Seq after integration
22:00 Performing differential accessibility analysis
26:19 Extracting fold changes for differentially accessible regions
27:40 Visualizing genomic regions of interest
30:36 Create interactive shiny genomic browser to visualize regions of interest
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 #signac #atacseq #atac #seurat #singlecell #singler #illumina #bridgeamplification #sequencingbysynthesis #multiplex #alleles #10x #oxfordnanopore #pacbio #affymetrix #barcode #setseed #reproducibility #pseudorandom #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
