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airpart

Differential cell-type-specific allelic imbalance

Bioconductor version: Release (3.17)

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")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("airpart")

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("airpart")
Differential allelic imbalance with airpart HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, CellBiology, ChIPSeq, Clustering, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, GraphAndNetwork, QualityControl, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, TranscriptomeVariant
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2 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
Linking To
Suggests knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr
System Requirements
Enhances
URL https://github.com/Wancen/airpart
Bug Reports https://github.com/Wancen/airpart/issues
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package airpart_1.8.0.tar.gz
Windows Binary airpart_1.8.0.zip
macOS Binary (x86_64) airpart_1.8.0.tgz
macOS Binary (arm64) airpart_1.8.0.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/
Package Downloads Report Download Stats