APL

Association Plots

Bioconductor version: Release (3.19)

APL is a package developed for computation of Association Plots (AP), a method for visualization and analysis of single cell transcriptomics data. The main focus of APL is the identification of genes characteristic for individual clusters of cells from input data. The package performs correspondence analysis (CA) and allows to identify cluster-specific genes using Association Plots. Additionally, APL computes the cluster-specificity scores for all genes which allows to rank the genes by their specificity for a selected cell cluster of interest.

Author: Clemens Kohl [cre, aut], Elzbieta Gralinska [aut], Martin Vingron [aut]

Maintainer: Clemens Kohl <kohl.clemens at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("APL")

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("APL")

Analyzing data with APL	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod
Version	1.8.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	GPL (>= 3)
Depends	R (>= 4.2)
Imports	reticulate, ggrepel, ggplot2, viridisLite, plotly, Seurat, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang, Matrix
System Requirements	python, pytorch, numpy
URL	https://vingronlab.github.io/APL/

Suggests	BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	APL_1.8.0.tar.gz
Windows Binary (x86_64)	APL_1.8.0.zip
macOS Binary (x86_64)	APL_1.8.0.tgz
macOS Binary (arm64)	APL_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/APL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/APL
Bioc Package Browser	https://code.bioconductor.org/browse/APL/
Package Short Url	https://bioconductor.org/packages/APL/
Package Downloads Report	Download Stats