iCellR

The software tool "iCellR" is a comprehensive toolkit designed to facilitate the analysis of data generated by single-cell sequencing technologies like scRNA-seq, scVDJ-seq, and CITE-Seq. The package, named Single (i) Cell R package ('iCellR'), offers a wide range of flexible functionalities across various analysis steps. These include normalization, clustering, dimensionality reduction, imputation, and visualization. Users have the flexibility to employ unsupervised and supervised models tailored to their specific research requirements. The toolkit incorporates interactive 2D and 3D visualizations, differential expression analysis, filters for cells, genes, and clusters, data merging, dropout normalization, imputation methods, batch correction, pathway analysis, identification of marker genes, cell type prediction, and pseudotime analysis.