Package: DenoIST 1.1.0

Aaron Kwok

DenoIST: DenoIST: Denoising Image-based Spatial Transcriptomics data

DenoIST identifies and removes contamination in Image-based Spatial Transcriptomics data, using a transposed poisson mixture model with local neighbourhood offsets to infer genes that are likely to be due to neighbourhood contamination rather than endogenous expression.

Authors:Aaron Kwok [aut, cre], Heejung Shim [aut], Davis McCarthy [aut]

DenoIST_1.1.0.tar.gz
DenoIST_1.1.0.zip(r-4.7)DenoIST_1.1.0.zip(r-4.6)DenoIST_1.1.0.zip(r-4.5)
DenoIST_1.1.0.tgz(r-4.6-any)DenoIST_1.1.0.tgz(r-4.5-any)
DenoIST_1.1.0.tar.gz(r-4.7-any)DenoIST_1.1.0.tar.gz(r-4.6-any)
DenoIST_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DenoIST/json (API)

# Install 'DenoIST' in R:

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

Bug tracker:https://github.com/aaronkwc/denoist/issues

On BioConductor:DenoIST-1.1.0(bioc 3.24)DenoIST-1.0.0(bioc 3.23)

software preprocessing spatial geneexpression singlecell transcriptomics

5.56 score 9 stars 7 scripts 188 downloads 4 exports 65 dependencies

Last updated from:35bfd0d4b0. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	177
linux-devel-x86_64	OK	632
source / vignettes	OK	513
linux-release-x86_64	OK	725
macos-release-arm64	OK	337
macos-oldrel-arm64	OK	316
windows-devel	OK	1010
windows-release	OK	1166
windows-oldrel	OK	1574
wasm-release	OK	165

Exports:denoist local_offset_distance_with_background local_offset_distance_with_background_fast solve_poisson_mixture

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob cachem cli cpp11 curl DBI dbplyr dbscan DelayedArray dplyr fastmap filelock flexmix generics GenomicRanges glue hexbin httr2 IRanges lattice lifecycle magick magrittr Matrix MatrixGenerics matrixStats memoise modeltools nnet openssl pbapply pillar pkgconfig purrr R6 rappdirs Rcpp rjson rlang RSQLite S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray sparseMatrixStats SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector

Denoising Imaged-based Spatial Transcriptomics data with DenoIST

Rendered fromdenoist_spe.Rmdusingknitr::rmarkdown

Last update: 2026-02-06
Started: 2025-05-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
DenoIST	denoist
Neighbourhood offset	local_offset_distance_with_background
Neighbourhood offset fast	local_offset_distance_with_background_fast
Poisson mixture model solver	solve_poisson_mixture