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:
STACAS_2.4.1.tar.gz
STACAS_2.4.1.zip(r-4.7)STACAS_2.4.1.zip(r-4.6)STACAS_2.4.1.zip(r-4.5)
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✨
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
- EnsemblGeneTable.Hs - Standardized gene list from ENSEMBL
- EnsemblGeneTable.Mm - Standardized gene list from ENSEMBL
- genes.blocklist - Genes blocklists for excluding HVGs
- sampleObj - Sample dataset to test STACAS installation
Last updated from:ea34e824e1. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 315 | ||
| source / vignettes | OK | 254 | ||
| linux-release-x86_64 | NOTE | 302 | ||
| macos-release-arm64 | NOTE | 240 | ||
| macos-oldrel-arm64 | NOTE | 169 | ||
| windows-devel | NOTE | 290 | ||
| windows-release | NOTE | 245 | ||
| windows-oldrel | NOTE | 251 | ||
| wasm-release | OK | 154 |
Exports:annotate.by.neighborsFindAnchors.STACASFindVariableFeatures.STACASIntegrateData.STACASPlotAnchors.STACASRun.STACASSampleTree.STACASStandardizeGeneSymbols
Dependencies:abindaskpassassortheadbase64encbeachmatBHBiocGenericsBiocNeighborsBiocParallelbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR.methodsS3R.ooR.utilsR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorsS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate by neighbors | annotate.by.neighbors |
| Standardized gene list from ENSEMBL (human) | EnsemblGeneTable.Hs |
| Standardized gene list from ENSEMBL (mouse) | EnsemblGeneTable.Mm |
| Find integration anchors using STACAS | FindAnchors.STACAS |
| FindVariableFeatures.STACAS | FindVariableFeatures.STACAS |
| Genes blocklists for excluding HVGs | genes.blocklist |
| IntegrateData.STACAS | IntegrateData.STACAS |
| PlotAnchors.STACAS | PlotAnchors.STACAS |
| Run the STACAS integration pipeline | Run.STACAS |
| Sample dataset to test STACAS installation | sampleObj |
| Integration tree generation | SampleTree.STACAS |
| Standardize gene symbols | StandardizeGeneSymbols |
