Reports markers list, differentially expressed genes, associated pathways, cell-type annotations, does batch correction and other related single cell analyses all wrapped within 'Seurat'.

Compute ploidy of single cells (or nuclei)
    based on single-cell (or single-nucleus)
    ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing)
    data <https://github.com/fumi-github/scPloidy>.

Add-on for the 'scan' package that creates plots 
  from single-case data frames ('scdf'). It includes functions for styling 
  single-case plots, adding phase-based lines to indicate various statistical 
  parameters, and predefined themes for presentations and publications. More 
  information and in depth examples can be found in the online book 
  "Analyzing Single-Case Data with R and 'scan" 
  Jürgen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.

Provide a workflow to jointly embed chromatin accessibility peaks and expressed genes into a shared low-dimensional space using paired single-cell ATAC-seq (scATAC-seq) and single-cell RNA-seq (scRNA-seq) data. It integrates regulatory relationships among peak-peak interactions (via 'Cicero'), peak-gene interactions (via Lasso, random forest, and XGBoost), and gene-gene interactions (via principal component regression). With the input of paired scATAC-seq and scRNA-seq data matrices, it assigns a low-dimensional feature vector to each gene and peak. Additionally, it supports the reconstruction of gene-gene network with low-dimensional projections (via epsilon-NN) and then the comparison of the networks of two conditions through manifold alignment implemented in 'scTenifoldNet'. See <doi:10.1093/bioinformatics/btaf483> for more details.

Useful to visualize the Poissoneity (an independent Poisson statistical framework, 
  where each RNA measurement for each cell comes from its own independent Poisson distribution) of 
  Unique Molecular Identifier (UMI) based single cell RNA sequencing (scRNA-seq) data, and explore 
  cell clustering based on model departure as a novel data representation.