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This is the development version of airpart; for the stable release version, see airpart.

Differential cell-type-specific allelic imbalance

Bioconductor version: Development (3.19)

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.

Author: Wancen Mu [aut, cre] , Michael Love [aut, ctb]

Maintainer: Wancen Mu <wancen at live.unc.edu>

Citation (from within R, enter citation("airpart")):


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Differential allelic imbalance with airpart HTML R Script
Reference Manual PDF


biocViews ATACSeq, CellBiology, ChIPSeq, Clustering, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, GraphAndNetwork, QualityControl, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, TranscriptomeVariant
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-2
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
System Requirements
URL https://github.com/Wancen/airpart
Bug Reports https://github.com/Wancen/airpart/issues
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Suggests knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr
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Source Package airpart_1.11.0.tar.gz
Windows Binary airpart_1.11.0.zip
macOS Binary (x86_64) airpart_1.11.0.tgz
macOS Binary (arm64) airpart_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/airpart
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/airpart
Bioc Package Browser https://code.bioconductor.org/browse/airpart/
Package Short Url https://bioconductor.org/packages/airpart/
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