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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/DenoIST/ |
| Package Short Url | https://bioconductor.org/packages/DenoIST/ |
| Package Downloads Report | Download Stats |