# 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](set-up-conda-environment.md)**
- **[Introduction to biocontainers and singularity](using-singularity.md)**
- **[Package installation using container-mod](container-mod.md)**
- **[Exploring Python Bioinformatics Packages with Jupyter Notebook](exploring-python-bioinformatics.md)**

## Project Organization & Best Practices

- **[How to Organize a Bioinformatics Project on the Tufts HPC](organizing-a-bioinformatics.md)**
- **[Getting started with bioinformatics tools](bioinformatics-tools-guide.md)**

## HPC & Parallel Computing

- **[Parallel Computing in R for Bioinformatics](parallel-computing-in-r.md)**
- **[Parallel Read Alignment on SLURM](parallel-read-alignment.md)**

## Workflow Management & Pipelines

- **[Running nfcore pipelines on Tufts HPC](running-nfcore-pipelines.md)**

## Bulk RNA-seq Analysis

- **[A Beginner’s Guide to Differential Expression Analysis with DESeq2 in R on Open OnDemand](de-seq2-in-r-ood.md)**

## Single-Cell & Spatial Transcriptomics

- **[scRNA-seq analysis with RStudio (Seurat)](sc-rna-seq-analysis-with-r.md)**
- **[A Practical Guide to Spatial Transcriptomics Analysis in R (MERFISH, 10x Visium, GeoMx DSP)](practical-guide-to-analyzing.md)**