Rvisdiff
Creates interactive graphs with 'R' for most popular differential expression methods
Science Score: 10.0%
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○Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○Scientific vocabulary similarity
Low similarity (6.5%) to scientific vocabulary
Keywords from Contributors
Repository
Creates interactive graphs with 'R' for most popular differential expression methods
Basic Info
- Host: GitHub
- Owner: BioinfoUSAL
- Language: JavaScript
- Default Branch: devel
- Size: 636 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Rvisdiff
Rvisdiff is an R/Bioconductor package which generates an interactive interface for the interpretation of differential analysis tests results. It generates a local Web page which enables the exploration of statistical analysis results with the generation of auto-analytical visualizations. The package supports as input the output of popular differential expression packages such as DESeq2, EdgeR and limma.
Install
```r
installing from bioconductor
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rvisdiff")
installing from github
library(devtools) install_github('BioinfoUSAL/Rvisdiff') ```
Usage
```r
Load example data
library("airway") data("airway") se <- airway se$dex <- relevel(se$dex, ref="untrt") countdata <- assay(se)
Differential expression analysis
library("DESeq2") dds <- DESeqDataSet(se, design = ~ cell + dex) dds <- DESeq(dds) dr <- results(dds, independentFiltering = FALSE)
Rvisdiff report generation
library("Rvisdiff") DEreport(dr, countdata, se$dex) ```
Owner
- Name: BioinfoUSAL
- Login: BioinfoUSAL
- Kind: user
- Location: Salamanca
- Company: University of Salamanca
- Website: http://bioinfo.usal.es
- Repositories: 1
- Profile: https://github.com/BioinfoUSAL
GitHub Events
Total
- Push event: 1
Last Year
- Push event: 1
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| BioinfoUSAL | b****o@u****s | 15 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y@u****m | 2 |
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 4,309 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 4
- Total maintainers: 1
bioconductor.org: Rvisdiff
Interactive Graphs for Differential Expression
- Homepage: https://github.com/BioinfoUSAL/Rvisdiff/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/Rvisdiff/inst/doc/Rvisdiff.pdf
- License: GPL-2 | GPL-3
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Latest release: 1.6.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.3.0 depends
- edgeR * imports
- utils * imports
- BiocManager * suggests
- BiocStyle * suggests
- DESeq2 * suggests
- SummarizedExperiment * suggests
- airway * suggests
- knitr * suggests
- limma * suggests
- matrixTests * suggests
- rmarkdown * suggests