R-universe search: topic:tumor-heterogeneity

Showing 3 of total 3 results (show query)

bioc

PureCN:Copy number calling and SNV classification using targeted short read sequencing

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Maintained by Markus Riester. Last updated 2 days ago.

copynumbervariation software sequencing variantannotation variantdetection coverage immunooncology bioconductor-package cell-free-dna copy-number loh tumor-heterogeneity tumor-mutational-burden tumor-purity

132 stars 9.88 score 40 scripts

bioc

TitanCNA:Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.

Maintained by Gavin Ha. Last updated 5 months ago.

sequencing wholegenome dnaseq exomeseq statisticalmethod copynumbervariation hiddenmarkovmodel genetics genomicvariation immunooncology 10x-genomics copy-number-variation genome-sequencing hmm tumor-heterogeneity

97 stars 8.47 score 68 scripts

hautaniemilab

jellyfisher:Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots

Generates interactive Jellyfish plots to visualize spatiotemporal tumor evolution by integrating sample and phylogenetic trees into a unified plot. This approach provides an intuitive way to analyze tumor heterogeneity and evolution over time and across anatomical locations. The Jellyfish plot visualization design was first introduced by Lahtinen, Lavikka, et al. (2023, <doi:10.1016/j.ccell.2023.04.017>). This package also supports visualizing ClonEvol results, a tool developed by Dang, et al. (2017, <doi:10.1093/annonc/mdx517>), for analyzing clonal evolution from multi-sample sequencing data. The 'clonevol' package is not available on CRAN but can be installed from its GitHub repository (<https://github.com/hdng/clonevol>).

Maintained by Kari Lavikka. Last updated 1 months ago.

visualization phylogenetics software spatial bioinformatics phylogenetic-analysis tumor-evolution tumor-heterogeneity visualization-tool

3 stars 5.18 score 2 scripts