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:Yue Lyu [aut, cre]

SCIntRuler_0.99.3.tar.gz
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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'))

Peer review:

Bug tracker:https://github.com/yuelyu21/scintruler/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

sequencinggeneticvariabilitysinglecell

5.04 score 2 stars 3 scripts 102 downloads 10 exports 188 dependencies

Last updated 1 months agofrom:fc21ad705a. Checks:OK: 1 ERROR: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-win-x86_64ERRORNov 14 2024
R-4.5-linux-x86_64ERRORNov 14 2024
R-4.4-win-x86_64ERRORNov 14 2024
R-4.4-mac-x86_64ERRORNov 14 2024
R-4.4-mac-aarch64ERRORNov 14 2024
R-4.3-win-x86_64ERRORNov 14 2024
R-4.3-mac-x86_64ERRORNov 14 2024
R-4.3-mac-aarch64ERRORNov 14 2024

Exports:CalcuSCIRcrossdistFindCellFindNNDistFindNNDistCGetClusterNormDataPermTestPlotSCIRSummCluster

Dependencies:abindaskpassassortheadbase64encbatchelorbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsbslibcachemcaToolscliclustercodetoolscoincolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsharmonyherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlibcoinlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImodeltoolsmultcompmunsellmvtnormnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2ResidualMatrixreticulateRhpcBLASctlrlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscattermoresctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensorTH.datatibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzlibbioczoo

Get Started with SCIntRuler

Rendered fromSCIntRuler.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-06-26
Started: 2024-01-17