Science Score: 13.0%
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○.zenodo.json file
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○Scientific vocabulary similarity
Low similarity (5.0%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Oshlack
- License: other
- Language: R
- Default Branch: main
- Size: 43.2 MB
Statistics
- Stars: 0
- Watchers: 8
- Forks: 0
- Open Issues: 0
- Releases: 3
Metadata Files
README.md
Damsel
The goal of Damsel is to conduct an end-to-end analysis for DamID. It takes an input of BAM files and a GATC region file and generates counts, identifies methylated regions, identifies peaks, associating peaks with genes, conducts gene ontology testing, and provides a variety of adjustable ggplot2 style visualisations.
Installation
You can install the development version of Damsel like so:
r
BiocManager::install("Oshlack/Damsel")
Example
Here we generate example results from the differential methylation results, and plot layers of raw counts and the logFC.
r
library(Damsel)
set.seed(123)
example_regions <- random_regions()
example_counts <- random_counts()
example_dm <- random_edgeR_results()
head(example_dm)
plotCounts(example_counts, "chr2L", 1, 5000) +
geom_dm(example_dm)
Owner
- Name: Oshlack
- Login: Oshlack
- Kind: organization
- Repositories: 38
- Profile: https://github.com/Oshlack
GitHub Events
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Last Year
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Caitlin Page | c****e@p****g | 404 |
| J Wokaty | j****y@u****m | 2 |
| Andrew Lonsdale | a****e@l****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 3,128 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 4
- Total maintainers: 1
bioconductor.org: Damsel
Damsel: an end to end analysis of DamID
- Homepage: https://github.com/Oshlack/Damsel
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/Damsel/inst/doc/Damsel.pdf
- License: MIT + file LICENSE
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Latest release: 1.4.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.50 depends
- AnnotationDbi * imports
- Biostrings * imports
- GenomeInfoDb * imports
- GenomicFeatures * imports
- GenomicRanges * imports
- Rsamtools * imports
- Rsubread * imports
- dplyr * imports
- edgeR * imports
- ggbio * imports
- ggplot2 * imports
- goseq * imports
- limma * imports
- magrittr * imports
- patchwork * imports
- plyranges * imports
- reshape2 * imports
- rlang * imports
- stats * imports
- stringr * imports
- tidyr * imports
- utils * imports
- BSgenome.Dmelanogaster.UCSC.dm6 * suggests
- TxDb.Dmelanogaster.UCSC.dm6.ensGene * suggests
- biomaRt * suggests
- biovizBase * suggests
- knitr * suggests
- org.Dm.eg.db * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests