DOI: 10.18129/B9.bioc.APL  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see APL.

Association Plots

Bioconductor version: 3.16

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")):


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biocViews DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
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
Suggests BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat
SystemRequirements python, pytorch, numpy
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package APL_1.2.0.tar.gz
Windows Binary APL_1.2.0.zip
macOS Binary (x86_64) APL_1.2.0.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/
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