Package: cardelino 1.7.0

Davis McCarthy

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.

Authors:Jeffrey Pullin [aut], Yuanhua Huang [aut], Davis McCarthy [aut, cre]

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# Install 'cardelino' in R:

install.packages('cardelino', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/single-cell-genetics/cardelino/issues

Datasets:

A_clone - A matrix of read numbers of alternative alleles for clone ID
A_germline - A matrix of read numbers of alternative alleles
Config_all - A list of tree configuration
D_clone - A matrix of sequencing depths for clone ID
D_germline - A matrix of sequencing depths
D_input - A matrix of sequencing depths
tree - A tree object
tree_3clone - A tree object
tree_4clone - A tree object
tree_5clone - A tree object

On BioConductor:cardelino-1.7.0(bioc 3.20)cardelino-1.6.0(bioc 3.19)

bioconductor-package

29 exports 0.61 score 120 dependencies

Last updated 2 months agofrom:abf5cef842

Exports:assign_cells_to_clones assign_scores binaryPRC binaryROC clone_id clone_id_EM clone_id_Gibbs colMatch donor_read_simulator get_snp_matrices get_tree heat_matrix load_cellSNP_vcf load_GT_vcf mixBinom mtx_to_df multiPRC plot_config_diffs plot_tree predMixBinom prob_heatmap pub.theme read_vcf rowArgmax rowMax sample_seq_depth sample_tree_SNV sim_read_count vc_heatmap

Dependencies:abind AnnotationDbi ape aplot askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli cluster codetools colorspace combinat cpp11 crayon curl DBI DelayedArray digest dplyr fansi farver fastmap formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggfun ggplot2 ggplotify ggtree glue gridGraphics gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise memuse mgcv mime munsell nlme openssl patchwork permute pheatmap pillar pinfsc50 pkgconfig plogr png purrr R6 RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow snpStats SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tidytree treeio UCSC.utils utf8 VariantAnnotation vcfR vctrs vegan viridisLite withr XML XVector yaml yulab.utils zlibbioc

Clone ID with cardelino

Davis McCarthy, Yuanhua Huang

Rendered fromvignette-cloneid.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2022-09-05
Started: 2018-07-25

Help page	Topics
A matrix of read numbers of alternative alleles for clone ID	A_clone
A matrix of read numbers of alternative alleles	A_germline
Assign cells to clones from cardelino results	assign_cells_to_clones
Scoring the simulation in assignment of singlets and doublets	assign_scores
Precision-recall curve for binary label prediction	binaryPRC
ROC curve for binary label prediction	binaryROC
Infer clonal identity of single cells	Clone ID clone_id clone_id_EM clone_id_Gibbs
Column match between two matrices by minimum mean absolute difference	colMatch
A list of tree configuration	Config_all
A matrix of sequencing depths for clone ID	D_clone
A matrix of sequencing depths	D_germline
A matrix of sequencing depths	D_input
Deviance Information Criterion for cardelino model	devianceIC
Reads simulator for donor identification	donor_read_simulator
Log likelihood of clone_id model It returns P(A, D \| C, I, theta0, theta1)	get_logLik
Get SNP data matrices from VCF object(s)	get_snp_matrices
Get a clonal tree from a configuration matrix	get_tree
Geweke diagnostic for MCMC sampling.	Geweke_Z
Plot heatmap from a matrix	heat_matrix
The theme of heatmaps for prob_heatmap and sites_heatmap	heatmap.theme
Load sparse matrices A and D from cellSNP VCF file with filtering SNPs	load_cellSNP_vcf
Load genotype VCF into numeric values: 0, 1, or 2	load_GT_vcf
EM algorithm for estimating binomial mixture model	mixBinom
Convert a matrix to data frame	mtx_to_df
Precision-recall curve for multi-class prediction	multiPRC
Define a publication-style plot theme	plot_config_diffs
Plot a phylogenetic tree	plot_tree
Predicted probability from learned binomial mixture model	predMixBinom
Plot a heatmap for probability of clone assignment	prob_heatmap
Define a publication-style plot theme	pub.theme
Read a VCF file into R session	read_vcf
Column index of the maximum value for each row in a matrix	rowArgmax
Maximum value for each row in a matrix	rowMax
Update matrix D with manually selected missing rate	sample_seq_depth
Down sample number of SNVs in the tree	sample_tree_SNV
Synthetic reads generator for genetic variants	sim_read_count
A tree object	tree
A tree object	tree_3clone
A tree object	tree_4clone
A tree object	tree_5clone
Plot a variant-cell heatmap for cell clonal assignment	vc_heatmap

Package: cardelino 1.7.0

cardelino: Clone Identification from Single Cell Data

Clone ID with cardelino

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