airpart

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see airpart.

Differential cell-type-specific allelic imbalance

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-5061-7581 , Michael Love [aut, ctb] ORCID iD ORCID: 0000-0001-8401-0545

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, CellBiology, ChIPSeq, Clustering, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, GraphAndNetwork, QualityControl, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, TranscriptomeVariant

Version 1.16.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 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

Suggests knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr

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Package Archives

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

Source Package airpart_1.16.0.tar.gz

Windows Binary (x86_64) airpart_1.16.0.zip

macOS Binary (x86_64) airpart_1.16.0.tgz

macOS Binary (arm64) airpart_1.16.0.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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