DenoIST

DenoIST: Denoising Image-based Spatial Transcriptomics data

Bioconductor version: 3.23 · Package version: 1.0.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DenoIST")

Details

Maintainer	Aaron Kwok <akwok@svi.edu.au>
Author	Aaron Kwok [aut, cre] (ORCID: <https://orcid.org/0000-0001-7831-4198>), Heejung Shim [aut], Davis McCarthy [aut]
License	MIT + file LICENSE
URL	https://github.com/aaronkwc/DenoIST
Bug Reports	https://github.com/aaronkwc/DenoIST/issues
Downloads rank	64
Source branch	RELEASE_3_23
biocViews	GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics

Documentation

Denoising Imaged-based Spatial Transcriptomics data with DenoIST

Download

Source package

Dependencies

Depends: R (>= 3.5.0)

Imports: flexmix, hexbin, pbapply, sparseMatrixStats, SpatialExperiment, stats, SummarizedExperiment, parallel, Matrix, dbscan, methods

Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, patchwork