airpart

DOI: 10.18129/B9.bioc.airpart    

Differential cell-type-specific allelic imbalance

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	ATACSeq, CellBiology, ChIPSeq, Clustering, DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, GraphAndNetwork, QualityControl, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, TranscriptomeVariant
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 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
LinkingTo
Suggests	knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr
SystemRequirements
Enhances
URL	https://github.com/Wancen/airpart
BugReports	https://github.com/Wancen/airpart/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	airpart_1.4.0.tar.gz
Windows Binary	airpart_1.4.0.zip
macOS Binary (x86_64)	airpart_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/airpart
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/airpart
Package Short Url	https://bioconductor.org/packages/airpart/
Package Downloads Report	Download Stats