Seurat

Scanpy is a Python-based single-cell analysis toolkit that provides similar functionalities to Seurat, including data preprocessing, dimensionality reduction, clustering, and differential expression analysis.

Monocle is another single-cell analysis toolkit, primarily focused on trajectory inference and pseudotime ordering of cells. While it offers overlapping functionalities with Seurat, its emphasis on trajectory analysis makes it a competitor in certain applications.

Cell Ranger is a widely used pipeline for processing raw sequencing data from 10x Genomics single-cell experiments, and its output can be directly used as input for Seurat. It is not a replacement for Seurat, but a tool used in the upstream data processing pipeline.

DESeq2 is a widely used package for differential expression analysis based on negative binomial models. While it's not single-cell specific, it can be applied to pseudobulk data generated from single-cell experiments analyzed with Seurat or other tools. Therefore, it complements Seurat's functionality in differential expression.

Snakemake is a workflow management system that can be used to automate and streamline single-cell analysis pipelines involving Seurat. It helps organize and execute complex workflows with dependencies, but it is not an analysis tool in itself.