CODEX: COpy number Detection by EXome sequencing (Bioconductor, vignettes)

Canopy: Copy number and single nucleotide mutation analysis of tumor phylogeny (GitHub, CRAN, vignettes)

SCALE: Single Cell ALlelic Expression (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 (GitHub, notebook)