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APL

Association Plots

Bioconductor version: Release (3.17)

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

Maintainer: Elzbieta Gralinska <gralinska at molgen.mpg.de>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 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
Linking To
Suggests BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat
System Requirements python, pytorch, numpy
Enhances
URL
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Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package APL_1.4.0.tar.gz
Windows Binary APL_1.4.0.zip
macOS Binary (x86_64) APL_1.4.0.tgz
macOS Binary (arm64) APL_1.4.0.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