DOI: 10.18129/B9.bioc.scAlign    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see scAlign.

An alignment and integration method for single cell genomics

Bioconductor version: 3.9

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")):


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


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PDF R Script alignment_tutorial
PDF   Reference Manual
Text   NEWS


biocViews DimensionReduction, NeuralNetwork, SingleCell, Software, Transcriptomics
Version 1.0.0
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
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Source Package scAlign_1.0.0.tar.gz
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