APL

DOI: 10.18129/B9.bioc.APL    

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

Association Plots

Bioconductor version: Development (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")):

Installation

To install this package, start R (version "4.2") 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

PDF   Reference Manual

Details

biocViews DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod
Version 1.1.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat
SystemRequirements python, pytorch, numpy
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary APL_1.1.0.zip
macOS 10.13 (High Sierra)
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

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