Package: SCIntRuler 0.99.3
SCIntRuler: Guiding the Integration of Multiple Single-Cell RNA-Seq Datasets
The accumulation of single-cell RNA-seq (scRNA-seq) studies highlights the potential benefits of integrating multiple datasets. By augmenting sample sizes and enhancing analytical robustness, integration can lead to more insightful biological conclusions. However, challenges arise due to the inherent diversity and batch discrepancies within and across studies. SCIntRuler, a novel R package, addresses these challenges by guiding the integration of multiple scRNA-seq datasets.
Authors:
SCIntRuler_0.99.3.tar.gz
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SCIntRuler_0.99.3.tgz(r-4.4-emscripten)
SCIntRuler.pdf |SCIntRuler.html✨
SCIntRuler/json (API)
# Install 'SCIntRuler' in R: |
install.packages('SCIntRuler', repos = c('https://yuelyu21.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yuelyu21/scintruler/issues
Pkgdown site:https://yuelyu21.github.io
- sim_data_sce - My Example Dataset
- sim_result - My Example Dataset
sequencinggeneticvariabilitysinglecellcpp
Last updated 5 months agofrom:fc21ad705a. Checks:1 OK, 10 ERROR. Indexed: yes.
Target | Result | Latest binary |
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Doc / Vignettes | OK | Feb 12 2025 |
R-4.5-win-x86_64 | ERROR | Feb 12 2025 |
R-4.5-mac-x86_64 | ERROR | Feb 12 2025 |
R-4.5-mac-aarch64 | ERROR | Feb 12 2025 |
R-4.5-linux-x86_64 | ERROR | Feb 12 2025 |
R-4.4-win-x86_64 | ERROR | Feb 12 2025 |
R-4.4-mac-x86_64 | ERROR | Feb 12 2025 |
R-4.4-mac-aarch64 | ERROR | Feb 12 2025 |
R-4.3-win-x86_64 | ERROR | Feb 12 2025 |
R-4.3-mac-x86_64 | ERROR | Feb 12 2025 |
R-4.3-mac-aarch64 | ERROR | Feb 12 2025 |
Exports:CalcuSCIRcrossdistFindCellFindNNDistFindNNDistCGetClusterNormDataPermTestPlotSCIRSummCluster
Dependencies:abindaskpassassortheadbase64encbatchelorbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsbslibcachemcaToolscliclustercodetoolscoincolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsharmonyherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenbaselibcoinlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImodeltoolsmultcompmunsellmvtnormnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2ResidualMatrixreticulateRhpcBLASctlrlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscattermoresctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensorTH.datatibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
SCIntRuler: Integration of Single-Cell RNA-seq Datasets | SCIntRuler-package SCIntRuler |
Calculate SCIntRuler | CalcuSCIR |
Cross-Distance Matrix Calculation | crossdist |
Find cells indicating shared biological features across conditions | FindCell |
Find the nearest neighbors | FindNNDist |
Find the nearest neighbors | FindNNDistC |
Get broad and fine clusters | GetCluster |
Normalized RNA data matrix | NormData |
Permutation Test | PermTest |
Plot SCIntRuler | PlotSCIR |
Input and Split SingleCellExperiment Data | SCEtoSeurat |
My Example Dataset | sim_data_sce |
My Example Dataset | sim_result |
Get maximum number of broad clusters | SummCluster |