scAlign

This package is for version 3.11 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: 3.11

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>

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

Installation

To install this package, start R (version "4.0") 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")

alignment_tutorial	PDF	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, NeuralNetwork, SingleCell, Software, Transcriptomics
Version	1.3.0
In Bioconductor since	BioC 3.9 (R-3.6) (5 years)
License	GPL-3
Depends	R (>= 3.5), SingleCellExperiment(>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN, PMA
Imports
System Requirements	python (< 3.7), tensorflow
URL	https://github.com/quon-titative-biology/scAlign
Bug Reports	https://github.com/quon-titative-biology/scAlign/issues

Suggests	knitr, rmarkdown, 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	scAlign_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/scAlign
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scAlign
Bioc Package Browser	https://code.bioconductor.org/browse/scAlign/
Package Short Url	https://bioconductor.org/packages/scAlign/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive