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

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SoupX.pdf |SoupX.html✨
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:

PBMC_metaData - PBMC 4K meta data
PBMC_sc - SoupChannel from PBMC data
scToy - Toy SoupChanel object

On CRAN:

15 exports 254 stars 6.27 score 146 dependencies 1 dependents 17 mentions 482 scripts 1.8k downloads

Last updated 2 years agofrom:8d89492306. Checks:OK: 6 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 22 2024
R-4.5-win	NOTE	Jul 23 2024
R-4.5-linux	OK	Aug 22 2024
R-4.4-win	OK	Aug 22 2024
R-4.4-mac	OK	Aug 22 2024
R-4.3-win	OK	Aug 22 2024
R-4.3-mac	OK	Aug 22 2024

Exports:adjustCounts autoEstCont calculateContaminationFraction estimateNonExpressingCells estimateSoup load10X plotChangeMap plotMarkerDistribution plotMarkerMap quickMarkers setClusters setContaminationFraction setDR setSoupProfile SoupChannel

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leiden lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

SoupX PBMC Demonstration

Matthew Daniel Young

Rendered frompbmcTutorial.Rmdusingknitr::rmarkdownon Aug 22 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Remove background contamination from count matrix	adjustCounts
Allocate values to "buckets" subject to weights and constraints	alloc
Automatically calculate the contamination fraction	autoEstCont
Calculate the contamination fraction	calculateContaminationFraction
Calculate which cells genuinely do not express a particular gene or set of genes	estimateNonExpressingCells
Get expression profile of soup	estimateSoup
Expands soup counts calculated at the cluster level to the cell level	expandClusters
Create Seurat style progress bar	initProgBar
Load a collection of 10X data-sets	load10X
PBMC 4K meta data	PBMC_metaData
SoupChannel from PBMC data	PBMC_sc
Plot maps comparing corrected/raw expression	plotChangeMap
Plots the distribution of the observed to expected expression for marker genes	plotMarkerDistribution
Plot ratio of observed to expected counts on reduced dimension map	plotMarkerMap
Plot correlation of expression profiles of soup and aggregated cells	plotSoupCorrelation
Print method for SoupChannel	print.SoupChannel
Gets top N markers for each cluster	quickMarkers
Toy SoupChanel object	scToy
Sets clustering for SoupChannel	setClusters
Manually set contamination fraction	setContaminationFraction
Manually set dimension reduction for a channel	setDR
Set soup profile	setSoupProfile
Construct a SoupChannel object	SoupChannel
SoupX: Profile, quantify and remove ambient RNA expression from droplet based RNA-seq	SoupX