scAlign

This package is for version 3.13 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: 3.13

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 "4.1") 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

Details

biocViews DimensionReduction, NeuralNetwork, SingleCell, Software, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-3
Depends R (>= 3.6), SingleCellExperiment(>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN
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
See More
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_1.6.0.tar.gz
Windows Binary scAlign_1.6.0.zip
macOS 10.13 (High Sierra) scAlign_1.6.0.tgz
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 3.13 Source Archive