https://github.com/bioconductor-source/seraster
Science Score: 26.0%
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○CITATION.cff file
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○.zenodo.json file
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Found 2 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 33.3 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Spatial Experiments raster (SEraster)
SEraster is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. This is the SEraster R documentation website. Questions, suggestions, or problems should be submitted as GitHub issues.
Overview
SEraster reduces the number of spatial points in spatial omics datasets for downstream analysis through a process of rasterization where single cells' gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. Here, we refer to a particular resolution of rasterization by the side length of the pixel such that finer resolution indicates smaller pixel size and coarser resolution indicates larger pixel size.
Installation
To install SEraster, we currently recommend using remotes:
r
require(remotes)
remotes::install_github('JEFworks-Lab/SEraster')
Tutorials
Introduction:
Citation
Our preprint describing SEraster is available on bioRxiv:
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
GitHub Events
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Dependencies
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- R >= 4.3.0 depends
- BiocParallel * imports
- Matrix * imports
- SpatialExperiment * imports
- SummarizedExperiment * imports
- ggplot2 * imports
- methods * imports
- rearrr * imports
- sf * imports
- CooccurrenceAffinity * suggests
- knitr * suggests
- nnSVG * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests