APL

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

Association Plots

Bioconductor version: Development (3.21)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("APL")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod
Version	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	GPL (>= 3)
Depends	R (>= 4.4.0)
Imports	basilisk, reticulate, Matrix, irlba, ggrepel, ggplot2, viridisLite, plotly, Seurat, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang
System Requirements	python, pytorch, numpy
URL	https://vingronlab.github.io/APL/

Suggests	BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/APL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/APL
Package Short Url	https://bioconductor.org/packages/APL/
Package Downloads Report	Download Stats