airpart
Differential cell-type-specific allelic imbalance
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("airpart")Details
| Maintainer | Wancen Mu <wancen@live.unc.edu> |
| Author | Wancen Mu [aut, cre] (ORCID: <https://orcid.org/0000-0002-5061-7581>), Michael Love [aut, ctb] (ORCID: <https://orcid.org/0000-0001-8401-0545>) |
| License | GPL-2 |
| URL | https://github.com/Wancen/airpart |
| Bug Reports | https://github.com/Wancen/airpart/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ATACSeq, CellBiology, ChIPSeq, Clustering, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, GraphAndNetwork, QualityControl, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, TranscriptomeVariant |
| Package Short Url | https://bioconductor.org/packages/airpart/ |
Citation
From within R, enter citation("airpart"):
Wancen Mu, Michael Love. airpart: Differential cell-type-specific allelic imbalance. doi:10.18129/B9.bioc.airpart, R package version 1.20.0, https://bioconductor.org/packages/airpart.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | airpart_1.20.0.tar.gz |
| Windows binary (x86_64) | airpart_1.20.0.zip |
| macOS binary (arm64) | airpart_1.20.0.tgz |
| macOS binary (x86_64) | airpart_1.20.0.tgz |
Dependencies
Depends: R (>= 4.1)
Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, scater, stats, smurf, apeglm (>= 1.13.3), emdbook, mclust, clue, dynamicTreeCut, matrixStats, dplyr, plyr, ggplot2, ComplexHeatmap, forestplot, RColorBrewer, rlang, lpSolve, grid, grDevices, graphics, utils, pbapply
Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr