Package: SeuratWrappers 0.4.0

Paul Hoffman

SeuratWrappers: Community-Provided Methods and Extensions for the Seurat Object

SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently.

Authors:Andrew Butler [aut], Saket Choudhary [ctb], David Collins [ctb], Yuhan Hao [ctb], Austin Hartman [ctb], Paul Hoffman [aut, cre], Gesmira Molla [ctb], Rahul Satija [aut], Tim Stuart [aut]

SeuratWrappers_0.4.0.tar.gz
SeuratWrappers_0.4.0.zip(r-4.7)SeuratWrappers_0.4.0.zip(r-4.6)SeuratWrappers_0.4.0.zip(r-4.5)
SeuratWrappers_0.4.0.tgz(r-4.6-any)SeuratWrappers_0.4.0.tgz(r-4.5-any)
SeuratWrappers_0.4.0.tar.gz(r-4.7-any)SeuratWrappers_0.4.0.tar.gz(r-4.6-any)
SeuratWrappers_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SeuratWrappers/json (API)

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

Bug tracker:https://github.com/satijalab/seurat-wrappers/issues

On CRAN:

Conda:

communitysingle-cell-analysissingle-cell-genomics

8.59 score 364 stars 4.2k scripts 24 exports 145 dependencies

Last updated from:ffaf74e306. Checks:7 ERROR, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR262
source / vignettesOK814
linux-release-x86_64ERROR422
macos-release-arm64ERROR186
macos-oldrel-arm64ERROR134
windows-develERROR390
windows-releaseERROR229
windows-oldrelERROR166
wasm-releaseOK454

Exports:ALRAChooseKPlotas.cell_data_setExportToCellbrowserFastMNNIntegrationPlotMiQCReadAlevinReadVelocityRunALRARunBanksyRunCoGAPSRunFastMNNRunGLMPCARunMiQCRunOptimizeALSRunPaCMAPRunPrestoRunPrestoAllRunQuantileAlignSNFRunQuantileNormRunSNFRuntricycleRunVelocityscVIIntegrationStopCellbrowser

Dependencies:abindaskpassbase64encBHBiocManagerbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLremotesreshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
SeuratWrappers: Community-Provided Methods and Extensions for the Seurat ObjectSeuratWrappers-package SeuratWrappers
ALRA Approximate Rank Selection PlotALRAChooseKPlot
Convert objects to Monocle3 'cell_data_set' objectsas.CellDataSet as.cell_data_set as.cell_data_set.Seurat
Extra conversions to Seurat objectsas.Seurat as.Seurat.cell_data_set as.Seurat.Conos as.Seurat.list
Export 'Seurat' objects for UCSC cell browser and stop open cell browser instances from RCellBrowser ExportToCellbrowser
Run fastMNN in Seurat 5FastMNNIntegration
used by ExportToCellbrowser: Return a matrix object from a Seurat object or show an error messagefindMatrix
Run 'link[monocle3]{learn_graph}' on a 'Seurat' objectLearnGraph
Run miQC on a Seurat objectPlotMiQC
Load alevin quantification dataReadAlevin
Load RNA Velocity data from a loom fileReadVelocity
Run Adaptively-thresholded Low Rank Approximation (ALRA)RunALRA RunALRA.default RunALRA.Seurat
Run Banksy on a Seurat ObjectRunBanksy
Run CoGAPs on a Seurat objectRunCoGAPS
Run fastMNNRunFastMNN
Run GLMPCARunGLMPCA
Run miQC on a Seurat objectRunMiQC
Run optimizeALS on a Seurat objectoptimizeALS RunOptimizeALS
Run PaCMAP (Pairwise Controlled Manifold Approximation)RunPaCMAP RunPaCMAP.default RunPaCMAP.Seurat
A Presto-based implementation of FindMarkers that runs Wilcoxon tests for the given identity classesRunPresto
A Presto-based implementation of FindAllMarkers that runs Wilcoxon tests for all identity classesRunPrestoAll RunPrestoAllNode
Run quantileAlignSNF on a Seurat objectquantileAlignSNF RunQuantileAlignSNF
Run quantile_norm on a Seurat objectquantile_norm RunQuantileNorm
Generate shared factor neighborhood graphRunSNF SNF
Run estimate_cycle_position on a Seurat objectRuntricycle
Run RNA VeloctyRunVelocity
scVI IntegrationscVIIntegration
Stop Cellbrowser web serverStopCellbrowser
Used by 'ExportToCellbrowser': Write a big sparse matrix to a .tsv.gz file by writing chunks, concating them with the Unix cat command, then gziping the result. This does not work on Windows, we'd have to use the copy /b command there.writeSparseTsvChunks