Package: demuxSNP 1.5.0
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:
demuxSNP_1.5.0.tar.gz
demuxSNP_1.5.0.zip(r-4.5)demuxSNP_1.5.0.zip(r-4.4)demuxSNP_1.5.0.zip(r-4.3)
demuxSNP_1.5.0.tgz(r-4.4-any)demuxSNP_1.5.0.tgz(r-4.3-any)
demuxSNP_1.5.0.tar.gz(r-4.5-noble)demuxSNP_1.5.0.tar.gz(r-4.4-noble)
demuxSNP_1.5.0.tgz(r-4.4-emscripten)demuxSNP_1.5.0.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
- 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-1.5.0(bioc 3.21)demuxSNP-1.4.0(bioc 3.20)
Last updated 2 months agofrom:5ce455e70e. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | OK | Dec 19 2024 |
| R-4.5-linux | OK | Dec 19 2024 |
| R-4.4-win | OK | Dec 19 2024 |
| R-4.4-mac | OK | Dec 19 2024 |
| R-4.3-win | OK | Dec 19 2024 |
| R-4.3-mac | OK | Dec 19 2024 |
Exports:add_snpscommon_geneshigh_conf_callsreassignreassign_balancedreassign_centroidreassign_jaccardsubset_vcf
Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclassclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydemuxmixdplyrensembldbfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehttrIRangesisobandjsonliteKEGGRESTKernelKnnlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngProtGenericsR6RColorBrewerRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryamlzlibbioc
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 |