Science Score: 36.0%
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
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 5 committers (40.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.6%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
extension of iSEE for TreeSE
Basic Info
- Host: GitHub
- Owner: microbiome
- Language: R
- Default Branch: devel
- Homepage: https://microbiome.github.io/iSEEtree/
- Size: 4.71 MB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 3
- Open Issues: 3
- Releases: 0
Topics
Metadata Files
README.md
iSEEtree
The goal of iSEEtree is to provide panel designs to explore hierarchical data stored in TreeSummarizedExperiment objects. This enables the interactive visualisation of microbiome data, cell lines and more.
Installation instructions
The release version of iSEEtree can be installed from Bioconductor as follows:
``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("iSEEtree") ```
Contributors or users interested in the latest functionality can install the devel version of iSEEtree as follows:
``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("iSEEtree") ```
Example
The basic functionality of iSEEtree can be explored as follows:
``` library(iSEEtree) library(mia) library(scater)
Import TreeSE
data("Tengeler2020", package = "mia") tse <- Tengeler2020
Add relabundance assay
tse <- transformAssay(tse, method = "relabundance")
Add reduced dimensions
tse <- runMDS(tse, assay.type = "relabundance")
Launch iSEE
if (interactive()) { iSEE(tse) } ```
Code of Conduct
Please note that the iSEEtree project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms. Contributions are welcome in the form of feedback, issues and pull requests. You can find the contributor guidelines of the miaverse here.
Acknowledgements
iSEEtree originates from the joint effort of the R/Bioconductor community. It is mainly based on the following software:
- R, statistical programming language [@core2024r]
- mia, framework for microbiome data analysis [@borman2024mia]
- iSEE, SummarizedExperiment interactive explorer [@rue2018isee]
- TreeSummarizedExperiment, S4 container for hierarchical data [@huang2021treesummarizedexperiment]
- shiny, web app development in R [@chang2024shiny]
Owner
- Name: microbiome
- Login: microbiome
- Kind: organization
- Email: microbiome-admin@googlegroups.com
- Location: Tools for microbiome analytics
- Website: microbiome.github.com
- Repositories: 35
- Profile: https://github.com/microbiome
Microbiome research methods
GitHub Events
Total
- Issues event: 11
- Watch event: 1
- Delete event: 9
- Issue comment event: 12
- Push event: 63
- Pull request event: 14
- Fork event: 1
- Create event: 7
Last Year
- Issues event: 11
- Watch event: 1
- Delete event: 9
- Issue comment event: 12
- Push event: 63
- Pull request event: 14
- Fork event: 1
- Create event: 7
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Giulio Benedetti | g****0@g****m | 144 |
| seraidarian | e****n@e****r | 48 |
| J Wokaty | j****y@s****u | 2 |
| A Wokaty | a****y@s****u | 2 |
| antagomir | l****i@i****i | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 22
- Total pull requests: 30
- Average time to close issues: 2 months
- Average time to close pull requests: 2 days
- Total issue authors: 3
- Total pull request authors: 3
- Average comments per issue: 1.45
- Average comments per pull request: 1.53
- Merged pull requests: 29
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 12
- Average time to close issues: 13 days
- Average time to close pull requests: 1 day
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 1.5
- Average comments per pull request: 0.17
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- RiboRings (15)
- LiNk-NY (1)
- danique-mulder (1)
Pull Request Authors
- RiboRings (31)
- ElySeraidarian (8)
- antagomir (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 3,012 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
bioconductor.org: iSEEtree
Interactive visualisation for microbiome data
- Homepage: https://github.com/microbiome/iSEEtree
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/iSEEtree/inst/doc/iSEEtree.pdf
- License: Artistic-2.0
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Latest release: 1.2.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- iSEEmiaViz * depends
- TreeSummarizedExperimentshiny * imports