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This is the development version of demuxSNP; for the stable release version, see demuxSNP.
Bioconductor version: Development (3.19)
This package assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. The SNP profile of each group os learned using high confidence assignments from the cell hashing data. Cells which cannot be assigned with high confidence from the cell hashing data are assigned to their most similar group based on their SNPs. We also provide some helper function to optimise SNP selection, create training data and merge SNP data into the SingleCellExperiment framework.
Author: Michael Lynch [aut, cre] , Aedin Culhane [aut]
Maintainer: Michael Lynch <michael.lynch at ul.ie>
Citation (from within R,
enter citation("demuxSNP")
):
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("demuxSNP")
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:
browseVignettes("demuxSNP")
HTML | R Script | Supervised Demultiplexing using Cell Hashing and SNPs |
Reference Manual | ||
Text | NEWS |
biocViews | Classification, SingleCell, Software |
Version | 1.1.2 |
In Bioconductor since | BioC 3.18 (R-4.3) (< 6 months) |
License | GPL-3 |
Depends | R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb |
Imports | MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges, Matrix, SummarizedExperiment, demuxmix, methods |
LinkingTo | |
Suggests | knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat |
SystemRequirements | |
Enhances | |
URL | https://github.com/michaelplynch/demuxSNP |
BugReports | https://github.com/michaelplynch/demuxSNP/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | demuxSNP_1.1.2.tar.gz |
Windows Binary | demuxSNP_1.1.2.zip (64-bit only) |
macOS Binary (x86_64) | demuxSNP_1.1.2.tgz |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/demuxSNP |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/demuxSNP |
Bioc Package Browser | https://code.bioconductor.org/browse/demuxSNP/ |
Package Short Url | https://bioconductor.org/packages/demuxSNP/ |
Package Downloads Report | Download Stats |
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