Single-Cell – Sangram Keshari Sahu

September 22, 2023

single-cell multi-omics scATAC-seq CITE-seq Seurat bioinformatics chromatin

Single-Cell Multi-omics Integration: Linking RNA, ATAC, and Protein Data

How to integrate scRNA-seq, scATAC-seq, and CITE-seq protein data using Seurat v5 and Muon — with a worked example covering alignment, joint embedding, and regulatory interpretation.

February 14, 2023

single-cell RNA-seq R bioinformatics

Single-Cell RNA-seq: A Practical Overview

An accessible introduction to scRNA-seq analysis — from raw reads to cell clusters — with notes on tooling and common pitfalls.

December 19, 2022

gene-regulatory-networks GRN single-cell SCENIC bioinformatics transcriptomics

Gene Regulatory Network Inference: Methods, Tools, and Pitfalls

A practical guide to inferring gene regulatory networks from single-cell and bulk RNA-seq data — comparing GENIE3, SCENIC, and GRNBoost2 with real code and honest caveats.

Tag: Single-Cell

Single-Cell Multi-omics Integration: Linking RNA, ATAC, and Protein Data

Single-Cell RNA-seq: A Practical Overview

Gene Regulatory Network Inference: Methods, Tools, and Pitfalls