DenoIST
This is the released version of DenoIST; for the devel version, see DenoIST.
DenoIST: Denoising Image-based Spatial Transcriptomics data
Bioconductor version: Release (3.23)
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.
Author: Aaron Kwok [aut, cre] 
, Heejung Shim [aut], Davis McCarthy [aut]
Maintainer: Aaron Kwok <akwok at svi.edu.au>
citation("DenoIST")):Aaron Kwok, Heejung Shim, Davis McCarthy. DenoIST: DenoIST: Denoising Image-based Spatial Transcriptomics data. doi:10.18129/B9.bioc.DenoIST, R package version 1.0.0, https://bioconductor.org/packages/DenoIST.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DenoIST")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DenoIST")| denoist_spe | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | flexmix, hexbin, pbapply, sparseMatrixStats, SpatialExperiment, stats, SummarizedExperiment, parallel, Matrix, dbscan, methods |
| System Requirements | |
| URL | https://github.com/aaronkwc/DenoIST |
| Bug Reports | https://github.com/aaronkwc/DenoIST/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, ggplot2, patchwork |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DenoIST_1.0.0.tar.gz |
| Windows Binary (x86_64) | DenoIST_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | DenoIST_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | DenoIST_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DenoIST |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DenoIST |
| Package Short Url | https://bioconductor.org/packages/DenoIST/ |
| Package Downloads Report | Download Stats |