NanoMethViz
Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.1%) to scientific vocabulary
Keywords from Contributors
Repository
Basic Info
- Host: GitHub
- Owner: Shians
- License: apache-2.0
- Language: R
- Default Branch: devel
- Homepage: https://shians.github.io/NanoMethViz/
- Size: 30.7 MB
Statistics
- Stars: 30
- Watchers: 3
- Forks: 4
- Open Issues: 37
- Releases: 0
Metadata Files
README.md
NanoMethViz
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NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing.
Installation
You can install NanoMethViz from Bioconductor with:
``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("NanoMethViz") ```
To install the latest developmental version, use:
``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(version='devel')
BiocManager::install("NanoMethViz") ```
Usage
This package currently works with data from dorado, megalodon, nanopolish and f5c, for information on how to use the package, please refer to the Users Guide.
Examples
MDS Plot
The MDS plot is used to visualise differences in the methylation profiles of multiple samples.
Feature Aggregation
The feature aggregation plot can average the methylation profiles across a set of features.
Region Methylation Plot
The region methylation plot can visualise the methylation profile of a region of interest. As well as provide a heatmap of the methylation along individual reads.
License
This project is licensed under Apache License, Version 2.0.
Owner
- Name: Shian Su
- Login: Shians
- Kind: user
- Location: Melbourne, Australia
- Company: Walter and Eliza Hall @WEHI_research
- Repositories: 120
- Profile: https://github.com/Shians
Bioinformatician, biostatistician and biological lifeform. Interested in R, C++ and Javascript for genomic data processing, summarisation and visualisation.
GitHub Events
Total
- Issues event: 15
- Watch event: 6
- Issue comment event: 42
- Push event: 28
- Fork event: 4
Last Year
- Issues event: 15
- Watch event: 6
- Issue comment event: 42
- Push event: 28
- Fork event: 4
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Shians | r****u@g****m | 578 |
| Shian Su | s****s@p****n | 13 |
| Nitesh Turaga | n****a@g****m | 8 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 53
- Total pull requests: 3
- Average time to close issues: about 2 months
- Average time to close pull requests: 4 days
- Total issue authors: 35
- Total pull request authors: 3
- Average comments per issue: 2.28
- Average comments per pull request: 0.67
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 14
- Pull requests: 0
- Average time to close issues: 10 days
- Average time to close pull requests: N/A
- Issue authors: 13
- Pull request authors: 0
- Average comments per issue: 1.07
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Shians (9)
- 0Bernhard (3)
- IdoBar (2)
- selmapichot (2)
- JWDebler (2)
- Qvdauwer (2)
- Machadum (2)
- dipannita-g (2)
- wietingj (2)
- YingziZhang-github (2)
- ralanany (2)
- faulk-lab (1)
- amootta (1)
- alanlorenzetti (1)
- ramnageena11 (1)
Pull Request Authors
- Shians (1)
- jeroen (1)
- madhav-madhusoodanan (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 10,916 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: NanoMethViz
Visualise methylation data from Oxford Nanopore sequencing
- Homepage: https://github.com/shians/NanoMethViz https://shians.github.io/NanoMethViz/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/NanoMethViz/inst/doc/NanoMethViz.pdf
- License: Apache License (>= 2.0)
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Latest release: 3.4.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0.0 depends
- ggplot2 * depends
- methods * depends
- AnnotationDbi * imports
- BiocSingular * imports
- GenomicRanges * imports
- RSQLite * imports
- Rcpp * imports
- Rsamtools * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- assertthat * imports
- bsseq * imports
- cpp11 >= 0.2.5 imports
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- e1071 * imports
- forcats * imports
- fs * imports
- ggrastr * imports
- glue * imports
- limma >= 3.44.0 imports
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- rlang * imports
- scales >= 1.2.0 imports
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- stats * imports
- stringr * imports
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- tidyr * imports
- utils * imports
- withr * imports
- zlibbioc * imports
- DSS * suggests
- Homo.sapiens * suggests
- Mus.musculus * suggests
- covr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
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