scAlign

DOI: 10.18129/B9.bioc.scAlign    

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

An alignment and integration method for single cell genomics

Bioconductor version: Development (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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
In Bioconductor since BioC 3.9 (R-3.6) (0.5 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
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_1.3.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) scAlign_1.3.0.tgz
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

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