CD4helper

CD4helper is an open-source software toolkit designed to help immunology researchers analyze datasets focused on CD4+ T helper cells. The project provides end-to-end support for single-cell and multispectral data, with an emphasis on identifying and characterizing CD4+ T cell subsets such as naive, memory, regulatory, and T follicular helper cells.

Core features include data import and quality control, normalization and batch correction, dimension reduction and clustering, automated annotation of CD4+ subsets using curated marker panels, differential expression analysis, and visualization tools such as UMAP and violin plots. It also supports trajectory inference to study differentiation pathways and gene-set enrichment analyses.

CD4helper is designed with a modular architecture to interoperate with established pipelines such as Scanpy and Seurat. It provides a Python API and a command-line interface, with optional R bindings, and is compatible with standard data structures such as AnnData and SeuratObjects. Documentation and tutorials accompany releases to support reproducible workflows.

The project is distributed under an open-source license and hosted on a public repository with documentation, example datasets, and tutorials. Development is community-driven, and users are encouraged to contribute. As with any single-cell workflow, results depend on data quality, annotation schemes, and parameter choices.

See also: CD4 T cell, T helper cells, single-cell RNA sequencing, immunology software tools.