DenoIST
This is the development version of DenoIST; to use it, please install the devel version of Bioconductor.
DenoIST: Denoising Image-based Spatial Transcriptomics data
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 0.99.2 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | flexmix, hexbin, pbapply, sparseMatrixStats, SpatialExperiment, stats, SummarizedExperiment, parallel |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DenoIST_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/DenoIST |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DenoIST |
| Bioc Package Browser | https://code.bioconductor.org/browse/DenoIST/ |
| Package Short Url | https://bioconductor.org/packages/DenoIST/ |
| Package Downloads Report | Download Stats |