Package: demuxSNP 1.11.0

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_1.11.0.tar.gz
demuxSNP_1.11.0.zip(r-4.7)demuxSNP_1.11.0.zip(r-4.6)demuxSNP_1.11.0.zip(r-4.5)
demuxSNP_1.11.0.tgz(r-4.6-any)demuxSNP_1.11.0.tgz(r-4.5-any)
demuxSNP_1.11.0.tar.gz(r-4.7-any)demuxSNP_1.11.0.tar.gz(r-4.6-any)
demuxSNP_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
demuxSNP/json (API)

# 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-1.11.0(bioc 3.24)demuxSNP-1.10.0(bioc 3.23)

classification singlecell

5.49 score 9 stars 23 scripts 8 exports 99 dependencies

Last updated from:b893e6de7a. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	301
linux-devel-x86_64	OK	644
source / vignettes	OK	463
linux-release-x86_64	OK	645
macos-release-arm64	OK	367
macos-oldrel-arm64	OK	323
windows-devel	OK	645
windows-release	OK	628
windows-oldrel	OK	558
wasm-release	OK	277

Exports:add_snps common_genes high_conf_calls reassign reassign_balanced reassign_centroid reassign_jaccard subset_vcf

Dependencies:abind AnnotationDbi AnnotationFilter askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo class cli codetools cpp11 crayon curl DBI DelayedArray demuxmix dplyr ensembldb farver fastmap formatR futile.logger futile.options generics GenomeInfoDb 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 mime openssl pillar pkgconfig png ProtGenerics R6 RColorBrewer Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml

Supervised Demultiplexing using Cell Hashing and SNPs

Rendered fromsupervised_demultiplexing.Rmdusingknitr::rmarkdown

Last update: 2024-10-03
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 based on SNPs	reassign_centroid
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