ExploreModelMatrix
Explore design matrices interactively with R/Shiny
Science Score: 36.0%
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Low similarity (13.0%) to scientific vocabulary
Keywords from Contributors
Repository
Explore design matrices interactively with R/Shiny
Basic Info
- Host: GitHub
- Owner: csoneson
- License: other
- Language: R
- Default Branch: devel
- Homepage: https://csoneson.github.io/ExploreModelMatrix/
- Size: 7.02 MB
Statistics
- Stars: 37
- Watchers: 6
- Forks: 2
- Open Issues: 5
- Releases: 2
Metadata Files
README.md
ExploreModelMatrix
ExploreModelMatrix is a small R package that lets the user interactively
explore a design matrix as generated by the model.matrix() R function.
In particular, given a table with sample information
and a design formula, ExploreModelMatrix illustrates the fitted values
from a general linear model (or, more generally, the value of the linear
predictor of a generalized linear model) for each combination of
input variables, simplifying understanding and generation of contrasts. A
number of other visualizations are also included in the interactive interface,
particularly simplifying the interpretation of linear models.
Installation
You can install ExploreModelMatrix from Bioconductor (note that you need
at least release 3.11 of Bioconductor, released in April 2020):
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ExploreModelMatrix")
Usage
The main function in the ExploreModelMatrix package is called
ExploreModelMatrix(). When calling ExploreModelMatrix(), simply provide a
data.frame (or DataFrame) with sample information and a design formula:
sampleData <- data.frame(genotype = rep(c("A", "B"), each = 4),
treatment = rep(c("ctrl", "trt"), 4))
ExploreModelMatrix(sampleData = sampleData,
designFormula = ~ genotype + treatment)
This will open up an R/Shiny application where you can explore the specified design matrix and the fitted values for each combination of predictor values.
For more examples of designs, we refer to the package vignette.
Owner
- Name: Charlotte Soneson
- Login: csoneson
- Kind: user
- Website: http://csoneson.github.io/
- Twitter: CSoneson
- Repositories: 110
- Profile: https://github.com/csoneson
GitHub Events
Total
- Watch event: 1
- Push event: 10
- Create event: 2
Last Year
- Watch event: 1
- Push event: 10
- Create event: 2
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Charlotte Soneson | c****n@g****m | 201 |
| Federico Marini | m****f@u****e | 28 |
| Nitesh Turaga | n****a@g****m | 10 |
| J Wokaty | j****y@s****u | 10 |
| A Wokaty | a****y@s****u | 2 |
| Peter Hickey | p****y@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 9
- Total pull requests: 26
- Average time to close issues: about 2 months
- Average time to close pull requests: about 16 hours
- Total issue authors: 5
- Total pull request authors: 3
- Average comments per issue: 1.44
- Average comments per pull request: 0.65
- Merged pull requests: 26
- 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
Top Authors
Issue Authors
- csoneson (4)
- llrs (2)
- mikelove (1)
- frederikziebell (1)
- federicomarini (1)
Pull Request Authors
- csoneson (17)
- federicomarini (8)
- PeteHaitch (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 15,233 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: ExploreModelMatrix
Graphical Exploration of Design Matrices
- Homepage: https://github.com/csoneson/ExploreModelMatrix
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/ExploreModelMatrix/inst/doc/ExploreModelMatrix.pdf
- License: MIT + file LICENSE
-
Latest release: 1.20.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- DT * imports
- MASS * imports
- S4Vectors * imports
- cowplot * imports
- dplyr * imports
- ggplot2 * imports
- limma * imports
- magrittr * imports
- methods * imports
- rintrojs * imports
- scales * imports
- shiny >= 1.5.0 imports
- shinydashboard * imports
- shinyjs * imports
- stats * imports
- tibble * imports
- tidyr * imports
- utils * imports
- BiocStyle * suggests
- htmltools * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 2.1.0 suggests
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- grimbough/bioc-actions/build-install-check v1 composite
- grimbough/bioc-actions/run-BiocCheck v1 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite