https://github.com/mikelove/spatialdmelxsim
Data from Combs and Fraser, "Spatially varying cis-regulatory divergence..." (2018)
https://github.com/mikelove/spatialdmelxsim
Last synced: 3 months ago
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Data from Combs and Fraser, "Spatially varying cis-regulatory divergence..." (2018)
- Host: GitHub
- URL: https://github.com/mikelove/spatialdmelxsim
- Owner: mikelove
- Created: 2021-06-16T05:40:31.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2021-08-01T05:57:52.000Z (almost 4 years ago)
- Last Synced: 2025-01-22T07:51:15.289Z (4 months ago)
- Language: R
- Homepage: https://bioconductor.org/packages/spatialDmelxsim
- Size: 190 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS
Awesome Lists containing this project
README
# spatialDmelxsim
Allelic counts from Combs & Fraser (2018), compiled into a
*SummarizedExperiment* object.
Package is available on Bioconductor as of August 2021:
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.
