numbat - Haplotype-Aware CNV Analysis from scRNA-Seq

A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.

Last updated 2 months ago

cancer-genomicscnv-detectionlineage-tracingphylogenysingle-cellsingle-cell-analysissingle-cell-rna-seqspatial-transcriptomics

7.16 score 166 stars 110 scripts 394 downloads

scistreer - Maximum-Likelihood Perfect Phylogeny Inference at Scale

Fast maximum-likelihood phylogeny inference from noisy single-cell data using the 'ScisTree' algorithm by Yufeng Wu (2019) <doi:10.1093/bioinformatics/btz676>. 'scistreer' provides an 'R' interface and improves speed via 'Rcpp' and 'RcppParallel', making the method applicable to massive single-cell datasets (>10,000 cells).

Last updated 1 years ago

evolutionphylogeneticssingle-cell

3.95 score 6 stars 1 packages 2 scripts 273 downloads

hahmmr - Haplotype-Aware Hidden Markov Model for RNA

Haplotype-aware Hidden Markov Model for RNA (HaHMMR) is a method for detecting copy number variations (CNVs) from bulk RNA-seq data. Additional examples, documentations, and details on the method are available at <https://github.com/kharchenkolab/hahmmr/>.

Last updated 1 years ago

2.18 score 1 packages 4 scripts 301 downloads