https://github.com/bioconductor-source/spatialdmelxsim
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 2 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (4.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 189 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
spatialDmelxsim
Allelic counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object.
Package is available on Bioconductor as of August 2021:
https://bioconductor.org/packages/spatialDmelxsim
After the package is released in October 2021:
BiocManager::install("spatialDmelxsim")
suppressPackageStartupMessages(library(SummarizedExperiment))
library(spatialDmelxsim)
se <- spatialDmelxsim()
The assays of se include a1 and a2. Here, a1 assay is the D
simulans allelic count, a2 assay is the D melanogaster allelic
count.
Data downloaded from GSE102233 as described in the publication:
Combs PA, Fraser HB (2018) Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic. PLOS Genetics 14(11): e1007631. https://doi.org/10.1371/journal.pgen.1007631
R scripts
- Script to build the SummarizedExperiment:
inst/scripts/make-data.R - Demo of loading the data and calculating allelic ratio:
vignettes/spatialDmelxsim.Rmd
Example figures of allelic ratio (simulans / total):
See vignette for details.
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
- ExperimentHub * depends
- R >= 4.1 depends
- SummarizedExperiment * depends
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests