DOI: 10.18129/B9.bioc.scAlign    

This is the development version of scAlign; to use it, please install the devel version of Bioconductor.

An alignment and integration method for single cell genomics

Bioconductor version: Development (3.10)

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>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script alignment_tutorial
PDF   Reference Manual
Text   NEWS


biocViews DimensionReduction, NeuralNetwork, SingleCell, Software, Transcriptomics
Version 1.1.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL-3
Depends R (>= 3.5)
Imports SingleCellExperiment(>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN
Suggests knitr, rmarkdown, testthat
SystemRequirements python (< 3.7), tensorflow
Depends On Me
Imports Me
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package scAlign_1.1.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) scAlign_1.1.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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