scAlign

DOI: 10.18129/B9.bioc.scAlign  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see scAlign.

An alignment and integration method for single cell genomics

Bioconductor version: 3.16

An unsupervised deep learning method for data alignment, integration and estimation of per-cell differences in -omic data (e.g. gene expression) across datasets (conditions, tissues, species). See Johansen and Quon (2019) for more details.

Author: Nelson Johansen [aut, cre], Gerald Quon [aut]

Maintainer: Nelson Johansen <njjohansen at ucdavis.edu>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scAlign")

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("scAlign")

 

PDF	R Script	alignment_tutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DimensionReduction, NeuralNetwork, SingleCell, Software, Transcriptomics
Version	1.12.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 years)
License	GPL-3
Depends	R (>= 3.6), SingleCellExperiment(>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN
Imports
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements	python (< 3.7), tensorflow
Enhances
URL	https://github.com/quon-titative-biology/scAlign
BugReports	https://github.com/quon-titative-biology/scAlign/issues
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	scAlign_1.12.0.tar.gz
Windows Binary	scAlign_1.11.0.zip
macOS Binary (x86_64)	scAlign_1.11.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/scAlign
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scAlign
Package Short Url	https://bioconductor.org/packages/scAlign/
Package Downloads Report	Download Stats