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
SCIntRuler_0.99.3.zip(r-4.5)SCIntRuler_0.99.3.zip(r-4.4)SCIntRuler_0.99.3.zip(r-4.3)
SCIntRuler_0.99.3.tgz(r-4.5-x86_64)SCIntRuler_0.99.3.tgz(r-4.5-arm64)SCIntRuler_0.99.3.tgz(r-4.4-x86_64)SCIntRuler_0.99.3.tgz(r-4.4-arm64)SCIntRuler_0.99.3.tgz(r-4.3-x86_64)SCIntRuler_0.99.3.tgz(r-4.3-arm64)
SCIntRuler_0.99.3.tar.gz(r-4.5-noble)SCIntRuler_0.99.3.tar.gz(r-4.4-noble)
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

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

On CRAN:

Conda:

sequencinggeneticvariabilitysinglecellcpp

4.85 score 2 stars 3 scripts 105 downloads 10 exports 187 dependencies

Last updated 5 months agofrom:fc21ad705a. Checks:1 OK, 10 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 12 2025
R-4.5-win-x86_64ERRORFeb 12 2025
R-4.5-mac-x86_64ERRORFeb 12 2025
R-4.5-mac-aarch64ERRORFeb 12 2025
R-4.5-linux-x86_64ERRORFeb 12 2025
R-4.4-win-x86_64ERRORFeb 12 2025
R-4.4-mac-x86_64ERRORFeb 12 2025
R-4.4-mac-aarch64ERRORFeb 12 2025
R-4.3-win-x86_64ERRORFeb 12 2025
R-4.3-mac-x86_64ERRORFeb 12 2025
R-4.3-mac-aarch64ERRORFeb 12 2025

Exports:CalcuSCIRcrossdistFindCellFindNNDistFindNNDistCGetClusterNormDataPermTestPlotSCIRSummCluster

Dependencies:abindaskpassassortheadbase64encbatchelorbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsbslibcachemcaToolscliclustercodetoolscoincolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsharmonyherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenbaselibcoinlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImodeltoolsmultcompmunsellmvtnormnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2ResidualMatrixreticulateRhpcBLASctlrlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscattermoresctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensorTH.datatibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo

Get Started with SCIntRuler

Rendered fromSCIntRuler.Rmdusingknitr::rmarkdownon Feb 12 2025.

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