Package: scMerge 1.21.0

Yingxin Lin

scMerge: scMerge: Merging multiple batches of scRNA-seq data

Like all gene expression data, single-cell data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple single-cell data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of single-cell data.

Authors:Yingxin Lin [aut, cre], Kevin Wang [aut], Sydney Bioinformatics and Biometrics Group [fnd]

scMerge_1.21.0.tar.gz
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scMerge.pdf |scMerge.html✨
scMerge/json (API)
NEWS

# Install 'scMerge' in R:
install.packages('scMerge', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sydneybiox/scmerge/issues

Datasets:
  • example_sce - Subsetted mouse ESC 'SingleCellExperiment' object
  • segList - Stably expressed gene list in official gene symbols for both human and mouse
  • segList_ensemblGeneID - Stably expressed gene list in EnsemblGeneID for both human and mouse

On BioConductor:scMerge-1.21.0(bioc 3.20)scMerge-1.20.0(bioc 3.19)

bioconductor-package

11 exports 1.16 score 178 dependencies 1 dependents 8 mentions

Last updated 2 months agofrom:4b2e3ee4aa

Exports:fastRUVIIIgetAdjustedMatruvSimulatesce_cbindscMergescMerge2scMerge2hscReplicatescRUVgscRUVIIIscSEGIndex

Dependencies:abindaskpassbackportsbase64encbatchelorbbmlebdsmatrixbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocallrcaToolscheckmatecliclustercodetoolscolorspacecpp11crayoncurlcvToolsdata.tableDelayedArrayDelayedMatrixStatsdensEstBayesDEoptimRdescdigestdistrdistributionaldqrngedgeRevaluatefansifarverfastmapFNNfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegplotsgridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphinlineIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalocfitlooM3DropmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimemunsellmvtnormnlmennetnumDerivopensslpheatmappillarpkgbuildpkgconfigpngposteriorprocessxproxyCpsQuickJSRR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppParallelRcppProgressreldistResidualMatrixrlangrmarkdownrobustbaserpartRSpectrarstanrstantoolsrstudioapirsvdRtsneruvS4ArraysS4VectorssassScaledMatrixscalesscaterscranscuttlesfsmiscSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsStanHeadersstartupmsgstatmodstringistringrSummarizedExperimentsyssystemfontstensorAtextshapingtibbletinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunXVectoryamlzlibbioc

An introduction to the scMerge package

Yingxin Lin, Kevin Y.X. Wang

Rendered fromscMerge.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-10-21
Started: 2018-08-09

An introduction to scMerge2

Yingxin Lin

Rendered fromscMerge2.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-08-02
Started: 2022-10-21