scAlign

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 ucdavis.edu>

Installation

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

if (!requireNamespace("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")

 

PDF	R Script	alignment_tutorial
PDF		Reference Manual
Text		NEWS

Details

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
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_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	scAlign_1.0.0.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