Cancer Genomics and Intratumor Heterogeneity

Canopy: Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing (CRAN, GitHub, vignettes)

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

Canopy2: Tumor phylogeny inference using bulk DNA and single-cell RNA sequencing (GitHub, vignettes)

Copy Number Variation

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

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

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

Single-Cell Omics

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

Destin: Toolkit for single-cell analysis of chromatin accessibility (GitHub, vignettes1, vignettes2)

Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility data (GitHub, vignettes1, vignettes2)

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

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

TRIPOD: Nonparametric interrogation of transcriptional regulation in single-cell RNA and chromatin accessibility multiomic data (GitHub, vignettes)

EPIC: Inferring relevant tissues and cell types for complex traits by integrating genome-wide association studies and single-cell RNA sequencing (GitHub, vignettes)

distQTL: Distribution quantitative trait loci identification by population-scale single-cell data (GitHub, vignettes)

DNA Damage, Repair, and Circadian Rhythm

Benchmarking methods for circadian rhythm detection: vignettes

DNA damage and excision repair: GitHub

Single-cell multiomic analysis of circadian rhythmicity: GitHub