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YouTubeTutorials

This repository holds scripts for demo tutorials on my youtube channel.

Script Youtube Video
dataManipulation.R How to manipulate gene expression data from NCBI GEO in R using dplyr
visualize_ggplot2.R Visualize gene expression data in R using ggplot2
dataformats.R Reading single-cell data in R: H5AD, loom, MEX, AnnData formats
singleCell_standard_workflow.R How to analyze single-cell RNA-Seq data in R
runDESeq2.R , getData.R DESeq2 workflow tutorial
singleCell_integration.R Integrate single-cell RNA-Seq datasets in R using Seurat (CCA)
singleCell_doublets.R DoubletFinder: Detect doublets in single-cell RNA-Seq data in R
microrray_RMA_normalize.R How to read and normalize microarray data in R - RMA normalization
singleCell_integrate_harmony.R Integrate single-cell RNA-Seq data in R using Harmony
singleCell_CI_markers.R Find markers and cluster identification in single-cell RNA-Seq using Seurat
singleCell_pseudoBulk.R Pseudo-bulk analysis for single-cell RNA-Seq data
convert_geneID_geneSymbols.R 3 ways to convert Ensembl IDs to gene symbols
RNASeqpipeline.sh Setup RNA-Seq Pipeline from scratch: fastq (reads) to counts
TI_monocle3.R Single-cell Trajectory analysis using Monocle3 and Seurat
WGCNA.R Weighted Gene Co-expression Network Analysis (WGCNA) Step-by-step Tutorial - Part 1 & Weighted Gene Co-expression Network Analysis (WGCNA) Step-by-step Tutorial - Part 2
variant_calling.sh WGS Variant Calling: Variant calling with GATK - Part 1
DESeq2ErrorFix.R DESeq2 Error Fix: DESeqDataSetFromMatrix ncol(countData) == nrow(colData) is not TRUE)
variant_filtering_annotation.sh WGS Variant Calling: Variant Filtering and Annotation - Part 2
installPackages.R How to install packages in R? What is CRAN? What is Bioconductor?
tcga_data_download.R Download data from GDC Portal using TCGAbiolinks R Package
KM_survival.R Survival analysis with TCGA data in R - Create Kaplan-Meier Curves
annotateSingleR.R Automatic cell-annotation for single-cell RNA-Seq data: A detailed SingleR tutorial (PART 1)
annotateSingleR_multipleRefs.R Automatic cell-annotation for single-cell RNA-Seq data: A detailed SingleR tutorial (PART 2)
setSeed.R Understanding set.seed in R: Ensuring Reproducibility in Data Analysis
conda and renv scripts Demystifying Conda (Anaconda, Miniconda and Bioconda) and Virtual Environments

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