Package: STACAS 2.4.1

Massimo Andreatta

STACAS: STACAS: Sub-Type Anchoring Correction for Alignment in Seurat

This package implements methods for batch correction and integration of scRNA-seq datasets, based on the popular Seurat anchor-based integration framework. In particular, STACAS is optimized for the integration of heterogenous datasets with only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods would tend to over-correct biological differences. The 2.0 version of our package allows to the users to incorporate explicit information about cell-types in order to assist the integration process.

Authors:Massimo Andreatta [aut, cre], Ariel Berenstein [aut], Josep Garnica [aut], Santiago Carmona [aut]

STACAS_2.4.1.tar.gz
STACAS_2.4.1.zip(r-4.7-any)STACAS_2.4.1.zip(r-4.6-any)STACAS_2.4.1.zip(r-4.5-any)
STACAS_2.4.1.tgz(r-4.6-any)STACAS_2.4.1.tgz(r-4.5-any)
STACAS_2.4.1.tar.gz(r-4.7-any)STACAS_2.4.1.tar.gz(r-4.6-any)
STACAS_2.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
STACAS/json (API)

# Install 'STACAS' in R:
install.packages('STACAS', repos = c('https://carmonalab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/carmonalab/stacas/issues

Datasets:

On CRAN:

Conda:

6.58 score 103 stars 1 packages 311 scripts 8 exports 164 dependencies

Last updated from:ea34e824e1. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE304
source / vignettesOK276
linux-releaseNOTE294
macos-releaseNOTE396
macos-oldrelNOTE379
windows-develNOTE243
windows-releaseNOTE234
windows-oldrelNOTE257
wasm-releaseOK169

Exports:annotate.by.neighborsFindAnchors.STACASFindVariableFeatures.STACASIntegrateData.STACASPlotAnchors.STACASRun.STACASSampleTree.STACASStandardizeGeneSymbols

Dependencies:abindaskpassassortheadbase64encbeachmatBHBiocGenericsBiocNeighborsBiocParallelbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR.methodsS3R.ooR.utilsR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppThreadRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorsS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo