Package: DenoIST 1.0.0

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_1.0.0.tar.gz
DenoIST_1.0.0.zip(r-4.7)DenoIST_1.0.0.zip(r-4.6)DenoIST_1.0.0.zip(r-4.5)
DenoIST_1.0.0.tgz(r-4.6-any)DenoIST_1.0.0.tgz(r-4.5-any)
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DenoIST_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DenoIST/json (API)
NEWS

# Install 'DenoIST' in R:
install.packages('DenoIST', repos = c('https://bioc-release.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)

softwarepreprocessingspatialgeneexpressionsinglecelltranscriptomics

5.65 score 9 stars 188 downloads 4 exports 65 dependencies

Last updated from:391d87bc67 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE183
linux-devel-x86_64OK572
source / vignettesOK431
linux-release-x86_64OK615
macos-release-arm64OK319
macos-oldrel-arm64OK260
windows-develOK1035
windows-releaseOK759
windows-oldrelOK792
wasm-releaseOK139

Exports:denoistlocal_offset_distance_with_backgroundlocal_offset_distance_with_background_fastsolve_poisson_mixture

Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrdbscanDelayedArraydplyrfastmapfilelockflexmixgenericsGenomicRangesgluehexbinhttr2IRangeslatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemodeltoolsnnetopensslpbapplypillarpkgconfigpurrrR6rappdirsRcpprjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector

Denoising Imaged-based Spatial Transcriptomics data with DenoIST

Aaron Kwok

Rendered fromdenoist_spe.Rmdusingknitr::rmarkdownon May 29 2026.

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

Readme and manuals

Help Manual

Help pageTopics
DenoISTdenoist
Neighbourhood offsetlocal_offset_distance_with_background
Neighbourhood offset fastlocal_offset_distance_with_background_fast
Poisson mixture model solversolve_poisson_mixture