Package: demuxSNP 1.3.0

Michael Lynch

demuxSNP: scRNAseq demultiplexing using cell hashing and SNPs

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.

Authors:Michael Lynch [aut, cre], Aedin Culhane [aut]

demuxSNP_1.3.0.tar.gz
demuxSNP_1.3.0.zip(r-4.5)demuxSNP_1.3.0.zip(r-4.4)demuxSNP_1.3.0.zip(r-4.3)
demuxSNP_1.3.0.tgz(r-4.4-any)demuxSNP_1.3.0.tgz(r-4.3-any)
demuxSNP_1.3.0.tar.gz(r-4.5-noble)demuxSNP_1.3.0.tar.gz(r-4.4-noble)
demuxSNP_1.3.0.tgz(r-4.4-emscripten)demuxSNP_1.3.0.tgz(r-4.3-emscripten)
demuxSNP.pdf |demuxSNP.html✨
demuxSNP/json (API)
NEWS

# Install 'demuxSNP' in R:

install.packages('demuxSNP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/michaelplynch/demuxsnp/issues

Datasets:

commonvariants_1kgenomes_subset - Sample vcf file
multiplexed_scrnaseq_sce - SingleCellExperiment object containing multiplexed RNA and HTO data from six biological smamples
vartrix_consensus_snps - Sample VarTrix output

On BioConductor:demuxSNP-1.3.0(bioc 3.20)demuxSNP-1.2.0(bioc 3.19)

bioconductor-package

7 exports 0.61 score 103 dependencies

Last updated 2 months agofrom:b9fcdaf88a

Exports:add_snps common_genes high_conf_calls reassign reassign_balanced reassign_jaccard subset_vcf

Dependencies:abind AnnotationDbi AnnotationFilter askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem class cli codetools colorspace cpp11 crayon curl DBI DelayedArray demuxmix dplyr ensembldb fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable httr IRanges isoband jsonlite KEGGREST KernelKnn labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png ProtGenerics R6 RColorBrewer Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales SingleCellExperiment snow SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml zlibbioc

Supervised Demultiplexing using Cell Hashing and SNPs

Michael Lynch, Aedin Culhane

Rendered fromsupervised_demultiplexing.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2023-05-02
Started: 2023-03-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add SNPs to SingleCellExperiment object	add_snps
Return a character vector of top n most frequent genes from a SingleCellExperiment object.	common_genes
Sample vcf file	commonvariants_1kgenomes_subset
Run demuxmix to determine high-confidence calls	high_conf_calls
SingleCellExperiment object containing multiplexed RNA and HTO data from six biological smamples	multiplexed_scrnaseq_sce
Reassign cells using knn	reassign
Reassign cells using balanced knn with jaccard distance	reassign_balanced
Reassign cells using knn with jaccard distance	reassign_jaccard
Subset common variants vcf file to only SNPs seen in 'top_genes'	subset_vcf
Sample VarTrix output	vartrix_consensus_snps