In alphabetical order …

For single cell data analysis:

Alleloscope (allele-specific copy number estimation for scDNA and scATAC sequencing) (Github)

cTP-Net (single cell Transcriptome to Protein prediction with deep neural network) (Github)

DENDRO (Genetic heterogeneity profiling by scRNA-seq) (Github)

DESCEND (Expression distribution deconvolution for single cell RNA-seq) (Github)

MUSIC (Bulk expression deconvolution with scRNA-seq reference) (Github)

SAVER (Gene expression imputation and denoising for single cell RNA sequencing) (Github)

SAVER-X (SAVER harnessing external data) (Github)

SCALE (Single cell allele-specific expression analysis)
(Github)

TASC (Toolkit for noise modeling in single cell RNA-seq with spike-ins)] (Github]

For copy number intra-tumor heterogeneity analysis:

CANOPY (Tumor phylogeny reconstruction by spatial and temporal bulk RNA sequencing) (CRAN)

FALCON (Allele-specific copy number estimation using whole genome sequencing data) (CRAN)

FALCON-X (Allele-specific copy number estimation using whole exome sequencing data) (CRAN)

CODEX/CODEX2 (statistical framework for full-spectrum CNV profiling in whole genome, whole exome, and targeted DNA sequencing) (Github)

iCNV (Integration across array and sequencing platforms for copy number detection) (Github)

MARATHON (Comprehensive pipeline for copy number profiling in normal and tumor samples) (Github)

SWAN (Structural variant profiling using paired-end genome sequencing data) (Bitbucket)

General statistical tools:

GCAT (Two-sample tests for categorical data utilizing similarity information among the categories) (CRAN)

GSEG (Change-point detection for multivariate data through a similarity graph on the observations) (CRAN)

LEAPP (Latent factor (“batch effect”) adjustment in multiple hypothesis testing) (CRAN)

SEMBLANCE (rank-semblance kernel for data compression, niche detection, and feature extraction) (CRAN)

SEQCBS (Segmentation and Bayesian confidence interval calculation for matched case/control point processes) (CRAN)