Science Score: 33.0%
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
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✓Academic publication links
Links to: ncbi.nlm.nih.gov -
✓Committers with academic emails
7 of 27 committers (25.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary
Keywords from Contributors
Repository
Genome data visualizations
Basic Info
- Host: GitHub
- Owner: griffithlab
- License: cc0-1.0
- Language: R
- Default Branch: master
- Size: 38 MB
Statistics
- Stars: 220
- Watchers: 19
- Forks: 64
- Open Issues: 64
- Releases: 0
Metadata Files
README.md
GenVisR
Please cite: "Skidmore et al. 2016 GenVisR: Genomic Visualizations in R Bioinformatics 32, 3012-3014" pubmed
Intuitively visualizing and interpreting data from high-throughput genomic technologies continues to be challenging. "Genomic Visualizations in R" (GenVisR) attempts to alleviate this burden by providing highly customizable publication-quality graphics supporting multiple species and focused primarily on a cohort level (i.e., multiple samples/patients). GenVisR attempts to maintain a high degree of flexibility while leveraging the abilities of ggplot2 and bioconductor to achieve this goal.
Install from Bioconductor
For the majority of users we recommend installing GenVisR from the release branch of Bioconductor, Installation instructions using this method can be found on the GenVisR landing page on Bioconductor.
Please note that GenVisR imports a few packages that have "system requirements", in most cases these requirements will already be installed. If they are not please follow the instructions to install these packages given in the R terminal. Briefly these packages are: "libcurl4-openssl-dev" and "libxml2-dev"
Development
Development for GenVisR occurs on the griffith lab github repository available here. For users wishing to contribute to development we recommend cloning the GenVisR repo there and submitting a pull request. Please note that development occurs on the R version that will be available at each Bioconductor release cycle. This ensures that GenVisR will be stable for each Bioconductor release but it may necessitate developers download R-devel.
We also encourage users to report bugs and suggest enhancements to GenVisR on the github issue page available here:
To install the latest development version of GenVisR (not recommended for most users):
```R
install and load devtools package
install.packages("devtools") library(devtools)
install GenVisR from github
install_github("griffithlab/GenVisR") ```
Vignettes
Documentation for GenVisR can be found on the bioconductor landing page in the form of vignettes available here GenVisR. Tutorials can also be found on biostars.org. Vignettes can also be viewed from within R.
```R
view vignettes
vignette(package="GenVisR") ```
Owner
- Name: The Griffith Lab
- Login: griffithlab
- Kind: organization
- Location: United States of America
- Website: https://griffithlab.org
- Repositories: 71
- Profile: https://github.com/griffithlab
Academic Lab of Obi and Malachi Griffith
GitHub Events
Total
- Issues event: 1
- Watch event: 11
- Issue comment event: 1
- Fork event: 2
- Create event: 1
Last Year
- Issues event: 1
- Watch event: 11
- Issue comment event: 1
- Fork event: 2
- Create event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Zach Skidmore | z****r@g****u | 685 |
| Alex H. Wagner | a****r@g****u | 51 |
| Alan O'Callaghan | a****n@o****m | 34 |
| z.skidmore | z****e@b****8 | 26 |
| Nitesh Turaga | n****a@g****m | 14 |
| Alan O'Callaghan | a****n@f****m | 10 |
| Katie Campbell | k****l@K****l | 9 |
| Obi Griffith | o****h@g****m | 8 |
| Jason kunisaki | j****i@C****l | 7 |
| J Wokaty | j****y@s****u | 6 |
| Dan Tenenbaum | d****a@f****g | 4 |
| Herve Pages | h****s@f****g | 4 |
| Malachi Griffith | m****g@g****m | 3 |
| Hervé Pagès | h****s@f****g | 3 |
| Jason kunisaki | j****i@c****u | 3 |
| Luca Beltrame | l****e@m****t | 2 |
| vobencha | v****a@g****m | 2 |
| Robert Lesurf | r****f@g****u | 2 |
| vobencha | v****n@r****g | 2 |
| mmoisse | m****e | 1 |
| Jim Java | j****a@r****g | 1 |
| Zach Skidmore | z****r@z****u | 1 |
| j.java | j****a@b****8 | 1 |
| baptiste | b****e | 1 |
| Joe Gage | j****e@n****u | 1 |
| Christian Brueffer | c****n@b****o | 1 |
| Avinash Ramu | t****h@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 71
- Total pull requests: 125
- Average time to close issues: 3 months
- Average time to close pull requests: about 1 hour
- Total issue authors: 7
- Total pull request authors: 5
- Average comments per issue: 1.18
- Average comments per pull request: 0.02
- Merged pull requests: 125
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 2.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- zlskidmore (15)
- ahwagner (10)
- kkrysiak (4)
- obigriffith (3)
- rlesurf (2)
- glscaglione (1)
- zpingfeng (1)
- tanbiswas (1)
- adam-cornwell (1)
- malachig (1)
- lfaino (1)
- eaferrante (1)
Pull Request Authors
- zlskidmore (41)
- ahwagner (13)
- kcampbel (6)
- rlesurf (2)
- gatoravi (1)
- joegage (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 3.3.0 depends
- methods * depends
- AnnotationDbi * imports
- BSgenome * imports
- BiocGenerics * imports
- Biostrings * imports
- DBI * imports
- FField * imports
- GenomeInfoDb * imports
- GenomicFeatures * imports
- GenomicRanges >= 1.25.4 imports
- IRanges >= 2.7.5 imports
- Rsamtools * imports
- VariantAnnotation * imports
- biomaRt >= 2.45.8 imports
- data.table * imports
- ggplot2 >= 2.1.0 imports
- gridExtra >= 2.0.0 imports
- gtable * imports
- gtools * imports
- plyr >= 1.8.3 imports
- reshape2 * imports
- scales * imports
- viridis * imports
- BSgenome.Hsapiens.UCSC.hg19 * suggests
- BSgenome.Hsapiens.UCSC.hg38 * suggests
- BiocStyle * suggests
- RMySQL * suggests
- TxDb.Hsapiens.UCSC.hg19.knownGene * suggests
- TxDb.Hsapiens.UCSC.hg38.knownGene * suggests
- formatR * suggests
- knitr * suggests
- rmarkdown * suggests
- roxygen2 * suggests
- testthat * suggests
- vdiffr * suggests