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APL

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

Association Plots


Bioconductor version: Development (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")

# 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

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

Details

biocViews DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod
Version 1.7.1
In Bioconductor since BioC 3.15 (R-4.2) (2 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
System Requirements python, pytorch, numpy
URL https://vingronlab.github.io/APL/
See More
Suggests BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat
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Package Archives

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

Source Package APL_1.7.1.tar.gz
Windows Binary APL_1.7.1.zip
macOS Binary (x86_64) APL_1.7.1.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/APL/
Package Short Url https://bioconductor.org/packages/APL/
Package Downloads Report Download Stats