Install monocle3 in R | Setup for Single-Cell RNA-Seq Analysis (ScRNAseq 1)
Welcome to ScRNAseq 1, the first video in our single-cell RNA sequencing series using R! 🧬
In this video, you’ll learn how to install and load the monocle3 package in R — a powerful tool for analyzing single-cell RNA-seq data, including trajectory inference, clustering, and dimensionality reduction.
🧠 What You’ll Learn:
✅ Step-by-step installation of monocle3 in R
✅ Install required dependencies (BiocManager, devtools, remotes)
✅ Fix common installation errors (HDF5, sparseMatrix, etc.)
✅ Verify and load the monocle3 package successfully
✅ Brief overview of monocle3 applications in single-cell analysis
📦 Installation Steps Covered:
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Step 1: Install Bioconductor manager
install.packages("BiocManager")
BiocManager::install()
Step 2: Install devtools (if not already installed)
install.packages("devtools")
Step 3: Install monocle3 from GitHub
devtools::install_github("cole-trapnell-lab/monocle3")
Step 4: Load the package
library(monocle3)
✅ Note: Ensure Rtools (Windows) or Xcode (macOS) is installed for successful compilation.
📌 Timestamps:
00:00 Introduction to monocle3
01:00 Install BiocManager and devtools
02:00 Install monocle3 from GitHub
03:00 Fix installation issues (compilers, dependencies)
04:30 Load and test monocle3
05:30 What's next in the ScRNAseq series
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