bioc-issue-bot
commented
2 years ago Hi @zijianni
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: SpotClean
Version: 0.99.3
Date: 2022/4/11
Title: SpotClean adjusts for spot swapping in spatial transcriptomics data
Authors@R: c(
person("Zijian", "Ni", role = c("aut", "cre"), email = "zni25@wisc.edu"),
person("Christina", "Kendziorski", role="ctb"))
Depends:
R (>= 4.0.0),
Imports:
stats,
methods,
utils,
dplyr,
S4Vectors,
SummarizedExperiment,
Matrix,
rhdf5,
ggplot2,
grid,
readbitmap,
rjson,
tibble,
viridis,
grDevices,
RColorBrewer,
Seurat
Suggests:
testthat (>= 2.1.0),
knitr,
BiocStyle,
rmarkdown,
R.utils
biocViews:
DataImport,
RNASeq,
Sequencing,
GeneExpression,
Spatial,
Transcriptomics,
Preprocessing
Description:
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.
License: GPL-3
NeedsCompilation: yes
VignetteBuilder: knitr
Encoding: UTF-8
SystemRequirements: C++11
RoxygenNote: 7.1.2
URL: https://github.com/zijianni/SpotClean
BugReports: https://github.com/zijianni/SpotClean/issues
drisso
zijianni
drighelli
lazappi
lshep
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