Tutorials - biostatsquid.com

Easy Gene Set Enrichment Analysis in R with fgsea()

by Biostatsquid | Sep 4, 2023 | Tutorials

A step-by-step R tutorial on performing Gene Set Enrichment Analysis with R package fgsea In this tutorial you will learn how to conduct Gene Set Enrichment Analysis (GSEA) using R-package fgsea. This package implements an algorithm for fast gene set enrichment...

Pathway Enrichment Analysis with clusterProfiler

by Biostatsquid | Jul 9, 2023 | Tutorials

R TUTORIAL: Perform pathway enrichment analysis with clusterProfiler() in R Table of contents 5 Before you start 5 Step-by-step clusterProfiler tutorial 9 Step 0: Set up your script and load the data 9 Step 1: Prepare inputs for clusterProfiler 9 Step 2: Run...

Easy R tutorial: pathway enrichment analysis plots

by Biostatsquid | Jul 9, 2023 | Tutorials

R TUTORIAL: Visualization of pathway enrichment analysis results with clusterProfiler Table of contents 5 Before you start 5 Step-by-step tutorial 9 Creating an enrichResult object 9 Barplots 9 Dotplots 9 Cnetplot 9 Heatplot 9 Treeplot 9 Enrichment map 9 Upsetplot 5...

Step-by-step heatmap tutorial with pheatmap()

by Biostatsquid | May 20, 2023 | Tutorials

R TUTORIAL: Follow this step-by-step heatmap tutorial with pheatmap() to visualise your differential gene expression results in R Table of contents 5 Before you start 5 Heatmaps with pheatmap(): complete script 5 Step-by-step guide to create annotated heatmaps in R 9...

Quality Check, Processing and Alignment of Sequencing Reads R tutorial

by Biostatsquid | Feb 8, 2023 | Tutorials

R TUTORIAL: From .fastq to .bam, preprocess and align your sequencing reads with this step-by-step sequencing reads R tutorial Table of contents 5 Before you start 5 Sequencing reads processing pipeline: complete script 5 Step-by-step guide for sequencing read...

Standard scRNAseq pre-processing workflow with Seurat

by Biostatsquid | Jan 10, 2023 | RNAseq, Tutorials

R TUTORIAL: Pre-process your scRNAseq data with this easy, step-by-step pipeline Table of contents 5 Before you start 5 scRNAseq pre-processing pipeline: complete script 5 Step-by-step guide to analyse your data with Seurat 9 Step 1: Set up your script 9 Step 2:...