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 (3.16)

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>

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

Installation

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

if (!require("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

PDF   Reference Manual

Details

biocViews DimensionReduction, NeuralNetwork, SingleCell, Software, Transcriptomics
Version 1.11.0
In Bioconductor since BioC 3.9 (R-3.6) (3.5 years)
License GPL-3
Depends R (>= 3.6), SingleCellExperiment(>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN
Imports
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
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
Package Short Url https://bioconductor.org/packages/scAlign/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: