Package: SoupX 1.6.2

Matthew Daniel Young

SoupX: Single Cell mRNA Soup eXterminator

Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.

Authors:Matthew Daniel Young

SoupX_1.6.2.tar.gz
SoupX_1.6.2.zip(r-4.7)SoupX_1.6.2.zip(r-4.6)SoupX_1.6.2.zip(r-4.5)
SoupX_1.6.2.tgz(r-4.6-any)SoupX_1.6.2.tgz(r-4.5-any)
SoupX_1.6.2.tar.gz(r-4.7-any)SoupX_1.6.2.tar.gz(r-4.6-any)
SoupX_1.6.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SoupX/json (API)

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

Bug tracker:https://github.com/constantamateur/soupx/issues

Datasets:

On CRAN:

Conda:

10.63 score 323 stars 1 packages 1.3k scripts 1.7k downloads 17 mentions 15 exports 142 dependencies

Last updated from:8d89492306. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK309
source / vignettesOK385
linux-release-x86_64OK300
macos-release-arm64OK212
macos-oldrel-arm64OK215
windows-develOK216
windows-releaseOK233
windows-oldrelOK236
wasm-releaseOK203

Exports:adjustCountsautoEstContcalculateContaminationFractionestimateNonExpressingCellsestimateSoupload10XplotChangeMapplotMarkerDistributionplotMarkerMapquickMarkerssetClusterssetContaminationFractionsetDRsetSoupProfileSoupChannel

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

SoupX PBMC Demonstration

Matthew Daniel Young

Rendered frompbmcTutorial.Rmdusingknitr::rmarkdownon May 11 2026.

Last update: 2022-05-26
Started: 2018-05-10