hammers

hammers provides a utilities suite for scRNA-seq data analysis compatible with both Seurat and SingleCellExperiment.

Key Features:

• Aggregate gene statistics retrieval: Retrieves aggregate gene statistics from scRNA-seq data.
• Rare gene detection and removal: Finds and removes rare genes from scRNA-seq datasets.
• Representation analysis: Performs representation analysis on scRNA-seq data.
• Center of mass computation: Computes the center of mass for the expression of a gene of interest in low-dimensional space.
• Silhouette calculation: Calculates silhouette and cluster-normalized silhouette for scRNA-seq data.

Scientific Applications:

• Single-cell RNA sequencing analysis: Supports scRNA-seq data analysis workflows using Seurat or SingleCellExperiment objects.
• Gene expression spatial analysis: Enables spatial characterization of gene expression patterns through center of mass computation in reduced-dimensional representations.
• Cluster quality assessment: Evaluates clustering performance using silhouette and cluster-normalized silhouette metrics.

Methodology:

The sources do not provide detailed methodological descriptions beyond the stated computational tasks.