APL
This is the development version of APL; for the stable release version, see APL.
Association Plots
DOI: 10.18129/B9.bioc.APL
Bioconductor version: Development (3.24)
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("APL")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.4.0) |
| Imports | Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly, SeuratObject, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang |
| System Requirements | |
| URL | https://vingronlab.github.io/APL/ |
See More
| Suggests | BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, sparseMatrixStats, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | APL_1.17.0.tar.gz |
| Windows Binary (x86_64) | APL_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | APL_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | APL_1.17.0.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 |