https://github.com/bioconductor-source/spicyr
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 27.3 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
spicyR
Spatial analysis of in situ cytometry data.
Overview
The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.
Installation
For the Bioconductor release version, run the following. ```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("spicyR") ```
If you would like the most up-to-date features, install the most recent development version. ```r
Install the development version from Bioconductor:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
The following initializes usage of Bioc devel
This will update all your Bioconductor packages to devel version
BiocManager::install(version='devel')
BiocManager::install("spicyR")
Otherwise install the development version from GitHub:
install.packages("devtools")
devtools::install_github("ellispatrick/spicyR") library(spicyR) ```
Submitting an issue or feature request
spicyR is still under active development. We would greatly appreciate any and
all feedback related to the package.
- R package related issues should be raised here.
- For general questions and feedback, please contact us directly via ellis.patrick@sydney.edu.au.
Authors
- Nicolas Canete
- Ellis Patrick - @TheEllisPatrick
Citation
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
- JamesIves/github-pages-deploy-action v4.5.0 composite
- actions/checkout v4 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- R >= 4.1 depends
- BiocParallel * imports
- ClassifyR * imports
- S4Vectors * imports
- SingleCellExperiment * imports
- SpatialExperiment * imports
- SummarizedExperiment * imports
- cli * imports
- concaveman * imports
- data.table * imports
- dplyr * imports
- ggforce * imports
- ggplot2 * imports
- grDevices * imports
- lmerTest * imports
- magrittr * imports
- methods * imports
- pheatmap * imports
- rlang * imports
- scam * imports
- spatstat.explore * imports
- spatstat.geom * imports
- stats * imports
- tibble * imports
- tidyr * imports
- BiocStyle * suggests
- imcRtools * suggests
- knitr * suggests
- pkgdown * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests