bioconductor-cardelino

name

bioconductor-cardelino

description

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 stoc

cardelino

Workflows

Standard Workflow

Assign cells to clones using scRNA-seq variant counts and a pre-defined clonal tree configuration.

library(cardelino)
library(ggplot2)

# 1. Load scRNA-seq variant data
vcf_file <- system.file("extdata", "cellSNP.cells.vcf.gz", package = "cardelino")
input_data <- load_cellSNP_vcf(vcf_file)

# 2. Load clonal tree configuration and align variant IDs
canopy_res <- readRDS(system.file("extdata", "canopy_results.coveraged.rds", package  
Config  canopy_restreeZ
rownamesConfig  gsub  rownamesConfig


set.seed
assignments  clone_idinput_dataA input_dataD Config  Config min_iter   max_iter  


df  assign_cells_to_clonesassignmentsprob


prob_heatmapassignmentsprob
heat_matrixtassignmentsConfig_prob  Config

AF  as.matrixinput_dataA  input_dataD
cardelinovc_heatmapAF assignmentsprob Config show_legend