cardelino
This is the development version of cardelino; for the stable release version, see cardelino.
Clone Identification from Single Cell Data
Bioconductor version: Development (3.24)
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.
Author: Jeffrey Pullin [aut], Yuanhua Huang [aut], Davis McCarthy [aut, cre]
Maintainer: Davis McCarthy <dmccarthy at svi.edu.au>
citation("cardelino")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("cardelino")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cardelino")| Clone ID with cardelino | HTML | R Script |
| Reference Manual |
Details
| biocViews | ExomeSeq, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-3 |
| Depends | R (>= 4.2), stats |
| Imports | combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR |
| System Requirements | |
| URL | https://github.com/single-cell-genetics/cardelino |
| Bug Reports | https://github.com/single-cell-genetics/cardelino/issues |
See More
| Suggests | BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM |
| Linking To | |
| Enhances | doMC |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cardelino_1.15.0.tar.gz |
| Windows Binary (x86_64) | cardelino_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | cardelino_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | cardelino_1.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cardelino |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cardelino |
| Bioc Package Browser | https://code.bioconductor.org/browse/cardelino/ |
| Package Short Url | https://bioconductor.org/packages/cardelino/ |
| Package Downloads Report | Download Stats |