Package: SpotClean 1.15.0

Zijian Ni

SpotClean: SpotClean adjusts for spot swapping in spatial transcriptomics data

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

Authors:Zijian Ni [aut, cre], Christina Kendziorski [ctb]

SpotClean_1.15.0.tar.gz
SpotClean_1.15.0.zip(r-4.7)SpotClean_1.15.0.zip(r-4.6)SpotClean_1.15.0.zip(r-4.5)
SpotClean_1.15.0.tgz(r-4.6-any)SpotClean_1.15.0.tgz(r-4.5-any)
SpotClean_1.15.0.tar.gz(r-4.7-any)SpotClean_1.15.0.tar.gz(r-4.6-any)
SpotClean_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpotClean/json (API)

# Install 'SpotClean' in R:

install.packages('SpotClean', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zijianni/spotclean/issues

Datasets:

mbrain_raw - Example 10x Visium spatial data: raw count matrix

On BioConductor:SpotClean-1.15.0(bioc 3.24)SpotClean-1.14.0(bioc 3.23)

dataimport rnaseq sequencing geneexpression spatial singlecell transcriptomics preprocessing rna-seq spatial-transcriptomics

6.74 score 38 stars 48 scripts 11 exports 177 dependencies

Last updated from:e4d13d631f. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	223
linux-devel-x86_64	OK	572
source / vignettes	OK	373
linux-release-x86_64	OK	553
macos-release-arm64	OK	326
macos-oldrel-arm64	OK	311
windows-devel	OK	491
windows-release	OK	507
windows-oldrel	OK	508
wasm-release	OK	220

Exports:arcScore convertToSeurat createSlide keepHighGene read10xRaw read10xRawH5 read10xSlide spotclean visualizeHeatmap visualizeLabel visualizeSlide

Dependencies:abind askpass base64enc BH Biobase BiocFileCache BiocGenerics biocmake bit bit64 bitops blob bmp bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table DBI dbplyr DelayedArray deldir digest dir.expiry dotCall64 dplyr dqrng evaluate farver fastDummies fastmap filelock fitdistrplus FNN fontawesome fs future future.apply generics GenomicRanges ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr httr2 ica igraph IRanges irlba isoband jpeg jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML readbitmap reshape2 reticulate rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown ROCR rprojroot RSpectra RSQLite Rtsne S4Arrays S4Vectors S7 sass scales scattermore sctransform Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo sourcetools sp spam SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tiff tinytex utf8 uwot vctrs viridis viridisLite withr xfun xtable XVector yaml zoo

SpotClean adjusts for spot swapping in spatial transcriptomics data

Rendered fromSpotClean.Rmdusingknitr::rmarkdown

Last update: 2023-04-10
Started: 2021-05-12

Help page	Topics
SpotClean: a computational method to adjust for spot swapping in spatial transcriptomics data	SpotClean-package SpotClean
Calculate the ambient RNA contamination (ARC) score	arcScore arcScore.default arcScore.SummarizedExperiment
Convert slide object to Seurat object	convertToSeurat
Create a new slide object	createSlide
Filter and return highly expressed or highly variable genes	keepHighGene
Example 10x Visium spatial data: raw count matrix	mbrain_raw
Read 10x Space Ranger output data	read10xRaw read10xRawH5 read10xSlide
Decontaminate spot swapping effect in spatial transcriptomics data	spotclean spotclean.SpatialExperiment spotclean.SummarizedExperiment
Visualize spot values on the 2D slide	visualizeHeatmap visualizeHeatmap.default visualizeHeatmap.SummarizedExperiment
Visualize spot labels on the 2D slide	visualizeLabel visualizeLabel.default visualizeLabel.SummarizedExperiment
Visualize the Visium slide image	visualizeSlide

Package: SpotClean 1.15.0

SpotClean: SpotClean adjusts for spot swapping in spatial transcriptomics data

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)