Package: SCIntRuler 0.99.8
SCIntRuler: Guiding the Integration of Multiple Single-Cell RNA-Seq Datasets
The accumulation of single-cell RNA sequencing (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' addresses these challenges by guiding the integration of multiple scRNA-seq datasets.
Authors:
SCIntRuler_0.99.8.tar.gz
SCIntRuler_0.99.8.zip(r-4.7-x86_64)SCIntRuler_0.99.8.zip(r-4.7-arm64)SCIntRuler_0.99.8.zip(r-4.6-x86_64)SCIntRuler_0.99.8.zip(r-4.6-arm64)SCIntRuler_0.99.8.zip(r-4.5-x86_64)
SCIntRuler_0.99.8.tgz(r-4.6-x86_64)SCIntRuler_0.99.8.tgz(r-4.6-arm64)SCIntRuler_0.99.8.tgz(r-4.5-x86_64)SCIntRuler_0.99.8.tgz(r-4.5-arm64)
SCIntRuler_0.99.8.tar.gz(r-4.7-arm64)SCIntRuler_0.99.8.tar.gz(r-4.7-x86_64)SCIntRuler_0.99.8.tar.gz(r-4.6-arm64)SCIntRuler_0.99.8.tar.gz(r-4.6-x86_64)
SCIntRuler_0.99.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
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/docs site:https://yuelyu21.github.io
- sim_data_sce - My Example Dataset
- sim_result - My Example Dataset
Last updated from:4ac21a071f. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 344 | ||
| linux-devel-x86_64 | OK | 418 | ||
| source / vignettes | OK | 354 | ||
| linux-release-arm64 | OK | 344 | ||
| linux-release-x86_64 | OK | 390 | ||
| macos-release-arm64 | OK | 395 | ||
| macos-release-x86_64 | OK | 498 | ||
| macos-oldrel-arm64 | OK | 367 | ||
| macos-oldrel-x86_64 | OK | 565 | ||
| windows-devel-arm64 | OK | 558 | ||
| windows-devel-x86_64 | OK | 357 | ||
| windows-release-arm64 | OK | 550 | ||
| windows-release-x86_64 | OK | 319 | ||
| windows-oldrel-x86_64 | OK | 341 | ||
| wasm-release | OK | 192 |
Exports:CalcuSCIRcrossdistFindCellFindNNDistFindNNDistCGetClusterNormDataPermTestPlotSCIRSCEtoSeuratSummCluster
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsbitopsbslibcachemcaToolscliclustercodetoolscoincommonmarkcowplotcpp11crosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsharmonyherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallibcoinlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUImodeltoolsmultcompmvtnormnlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulateRhpcBLASctlrlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorsS7sandwichsassscalesscattermoresctransformSeqinfoSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensorTH.datatibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo
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 |