rajarshiray25/bioinformatics-workflows

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
scATACSeq_standard_workflow.R	How to analyze single-cell ATAC-Seq data in R; Detailed Signac Workflow Tutorial
scATACSeq_downstream_workflow.R	Comprehensive Guide to Downstream Analysis for Single-Cell ATAC-Seq in R - scATAC-Seq Workflow
interactionTerms.R	DESeq2 Design Explained: Understanding Interaction Terms in RNA-Seq Analysis