davismcc/cardelino: Clone Identification from Single Cell Data

Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

Getting started

Package details

Bioconductor views ExomeSeq GeneExpression RNASeq Sequencing SingleCell Software Transcriptomics Visualization
Maintainer
LicenseGPL-3
Version1.1.1
URL https://github.com/single-cell-genetics/cardelino
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("davismcc/cardelino")
davismcc/cardelino documentation built on Nov. 19, 2022, 2:44 a.m.