CODEX: A normalization and copy number variation detection method for whole exome sequencing (Bioconductor, GitHub, vignettes)

Canopy: Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing (CRAN, GitHub, vignettes)

SCALE: Modeling allele-specific gene expression by single-cell RNA sequencing (GitHub, vignettes)

CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing (GitHub, notebook)

Falcon-X: Allele-specific copy number estimation by whole-exome sequencing (CRAN)

MARATHON: Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny (GitHub, notebook)

Destin: Toolkit for single-cell analysis of chromatin accessibility (GitHub, notebook1, notebook2)

SCOPE: A normalization and copy number estimation method for single-cell DNA sequencing (Bioconductor, GitHub, notebook)

SCDC: Deconvolution of bulk gene expression by single-cell RNA sequencing data (GitHub, notebook)