Bioinformatics Tutorials

Maintained by:

Shirley Li, Bioinformatician, xue.li37@tufts.edu

Yucheng Zhang, Senior Bioinformatics Engineer, yucheng.zhang@tufts.edu

TTS Research Technology

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A curated collection of practical, reproducible bioinformatics tutorials for researchers working on the Tufts HPC. These guides focus on real-world analysis workflows — from RNA-seq and spatial transcriptomics to workflow management and high-performance computing — designed to help you move from raw data to interpretable results efficiently and reproducibly.

Getting Started

For users new to Tufts HPC or bioinformatics.

• Set Up Conda Environment and Create Jupyter Kernel for scRNA-seq Analysis

• Introduction to biocontainers and singularity

• Package installation using container-mod

• Exploring Python Bioinformatics Packages with Jupyter Notebook

Project Organization & Best Practices

• How to Organize a Bioinformatics Project on the Tufts HPC

• Getting started with bioinformatics tools

HPC & Parallel Computing

• Parallel Computing in R for Bioinformatics

• Parallel Read Alignment on SLURM

Workflow Management & Pipelines

• Running nfcore pipelines on Tufts HPC

Bulk RNA-seq Analysis

• A Beginner’s Guide to Differential Expression Analysis with DESeq2 in R on Open OnDemand

Single-Cell & Spatial Transcriptomics

• scRNA-seq analysis with RStudio (Seurat)

• A Practical Guide to Spatial Transcriptomics Analysis in R (MERFISH, 10x Visium, GeoMx DSP)