ISCB SC RSG-Nigeria Workshop - Bioinformatics for Single-Cell Classification
ISCB-SC RSG-Nigeria is excited to host an immersive workshop on Bioinformatics for Single-Cell Classification, with our lead facilitator: Aneesa Valentine, Senior SciOps Engineer at DataJoint.
Single-cell RNA-seq analysis has long relied on dimensionality reduction techniques like PCA to power downstream tasks such as cell type classification. But foundation models like Geneformer are changing what’s possible, offering rich, pretrained embeddings that can be used as features in place of (or alongside) traditional methods.
In this hands-on workshop, you’ll work through a complete single-cell analysis pipeline using the classic PBMC 3k dataset (via Scanpy). We’ll start with the fundamentals, quality control and clustering, before moving into a head-to-head comparison: how well does a simple logistic regression classifier perform when trained on Geneformer embeddings versus traditional PCA components?
What you’ll learn:
Core single-cell QC and clustering workflow using Scanpy
How to generate cell embeddings using Geneformer, a single-cell foundation model
How to train and evaluate a logistic regression classifier for cell type prediction
A practical, code-first comparison of classical vs. foundation-model-derived features
Who this is for:
This session is designed for students and early-career researchers with some familiarity with Python. No prior single-cell or foundation model experience required, we’ll build up the concepts as we go.
What to bring:
A laptop with Google Colab access (or your preferred Python development environment). We’ll provide the notebook.
Speaker: Aneesa Valentine
Senior SciOps Engineer, DataJoint
Aneesa is a Senior SciOps Engineer at DataJoint, where she specializes in building infrastructure that supports deterministic agentic workflows in life science R&D.
Aneesa’s expertise is rooted in a deep understanding of both biological data and the computational constraints researchers face in the field. Having transitioned from computational genomics research into the engineering and infrastructure space, she possesses a unique perspective on the tools that enable modern scientific breakthroughs.
Beyond her engineering role, Aneesa is a passionate advocate for scientific literacy. She founded ImpaktBio, an educational and training company helping R&D teams work with biological data at scale. With her Substack, she explores the practical skills that are often overlooked in formal training. Aneesa is known for her ability to translate complex technical concepts into clear, intuitive explanations and thrives in learning and development environments that encourage critical thinking, curiosity and creative problem-solving.