Package: scMerge 1.23.0
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:
scMerge_1.23.0.tar.gz
scMerge_1.23.0.zip(r-4.5)scMerge_1.23.0.zip(r-4.4)scMerge_1.23.0.zip(r-4.3)
scMerge_1.23.0.tgz(r-4.4-any)scMerge_1.23.0.tgz(r-4.3-any)
scMerge_1.23.0.tar.gz(r-4.5-noble)scMerge_1.23.0.tar.gz(r-4.4-noble)
scMerge_1.23.0.tgz(r-4.4-emscripten)scMerge_1.23.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/sydneybiox/scmerge/issues
- 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-1.23.0(bioc 3.21)scMerge-1.22.0(bioc 3.20)
batcheffectgeneexpressionnormalizationrnaseqsequencingsinglecellsoftwaretranscriptomicsbioinformaticssingle-cell
Last updated 2 months agofrom:d99a8f2635. Checks:OK: 2 NOTE: 4 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 09 2024 |
| R-4.5-win | NOTE | Dec 09 2024 |
| R-4.5-linux | NOTE | Dec 09 2024 |
| R-4.4-win | NOTE | Dec 09 2024 |
| R-4.4-mac | NOTE | Dec 09 2024 |
| R-4.3-win | OK | Dec 09 2024 |
| R-4.3-mac | ERROR | Dec 09 2024 |
Exports:fastRUVIIIgetAdjustedMatruvSimulatesce_cbindscMergescMerge2scMerge2hscReplicatescRUVgscRUVIIIscSEGIndex
Dependencies:abindaskpassassortheadbackportsbase64encbatchelorbbmlebdsmatrixbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocallrcaToolscheckmatecliclustercodetoolscolorspacecpp11crayoncurlcvToolsdata.tableDelayedArrayDelayedMatrixStatsdensEstBayesDEoptimRdescdigestdistrdistributionaldqrngedgeRevaluatefansifarverfastmapFNNfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegplotsgridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphinlineIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalocfitlooM3DropmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimemunsellmvtnormnlmennetnumDerivopensslpheatmappillarpkgbuildpkgconfigpngposteriorprocessxproxyCpsQuickJSRR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppParallelRcppProgressreldistResidualMatrixrlangrmarkdownrobustbaserpartRSpectrarstanrstantoolsrstudioapirsvdRtsneruvS4ArraysS4VectorssassScaledMatrixscalesscaterscranscuttlesfsmiscSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsStanHeadersstartupmsgstatmodstringistringrSummarizedExperimentsyssystemfontstensorAtextshapingtibbletinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunXVectoryamlzlibbioc
