scAlign
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see scAlign.
An alignment and integration method for single cell genomics
Bioconductor version: 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)
Author: Nelson Johansen [aut, cre], Gerald Quon [aut]
Maintainer: Nelson Johansen <njjohansen at ucdavis.edu>
citation("scAlign")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("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")| alignment_tutorial | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DimensionReduction, NeuralNetwork, SingleCell, Software, Transcriptomics |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (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 | |
| System Requirements | python (< 3.7), tensorflow |
| URL | https://github.com/quon-titative-biology/scAlign |
| Bug Reports | https://github.com/quon-titative-biology/scAlign/issues |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scAlign_1.12.0.tar.gz |
| Windows Binary | scAlign_1.11.0.zip |
| macOS Binary (x86_64) | scAlign_1.11.0.tgz |
| macOS Binary (arm64) | |
| 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 |
| Old Source Packages for BioC 3.16 | Source Archive |