shinyMethyl
Interactive visualization of Illumina methylation array data
Science Score: 36.0%
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Low similarity (11.0%) to scientific vocabulary
Keywords from Contributors
Repository
Interactive visualization of Illumina methylation array data
Statistics
- Stars: 6
- Watchers: 1
- Forks: 0
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
shinyMethyl
|Package|BioC-release|BioC-devel
|---|---|---|
|shinyMethyl|
|
|shinyMethylData|
|
Authors: Jean-Philippe Fortin and Kasper Daniel Hansen
Welcome to shinyMethyl, an interactive R application based on the shiny package for exploration of DNA methylation data from Illumina arrays (450k and EPIC arrays). shinyMethyl is part of the Bioconductor project.
The shinyMethyl paper can be found here
Installation
First, you will need to install at least the following packages from Bioconductor
{r}
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("minfi")
BiocManager::install("minfiData")
and from CRAN
{r}
install.packages("httpuv")
install.packages("devtools")
install.packages("matrixStats")
install.packages("RColorBrewer")
To install the development version of shinyMethyl:
{r}
library(devtools)
install_github("rstudio/shiny")
install_github("jfortin1/shinyMethyl")
install_github("jfortin1/shinyMethylData")
Vignette
You can find the vignette for shinyMethyl at https://github.com/Jfortin1/shinyMethyl/blob/master/vignettes/shinyMethyl.pdf
Quick example
After installation, you can launch shinyMethyl with an example dataset from TCGA with the following code:
{r}
library(shinyMethyl)
library(shinyMethylData)
runShinyMethyl(summary.tcga.raw, summary.tcga.norm)
Citation
To cite package shinyMethyl in publications use:
Fortin J, Fertig EJ and Hansen KD (2014). “shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.”, F1000Research
A BibTeX entry for LaTeX users is
@Article{shinymethyl, author = {Jean-Philippe Fortin and Elana J. Fertig and Kasper D. Hansen}, title = {{shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R}}, journal = {F1000Research}, year = {2014}, volume = {3}, pages = {175}, doi = {10.12688/f1000research.4680.2}, pubmed = {25285208} }
Owner
- Name: Jean-Philippe Fortin
- Login: Jfortin1
- Kind: user
- Location: San Francisco
- Company: Genentech
- Website: https://scholar.google.com/citations?user=cpVxkJIAAAAJ&hl=en
- Repositories: 48
- Profile: https://github.com/Jfortin1
Senior Principal Scientist @ Genentech
GitHub Events
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- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jean-Philippe Fortin | j****n@j****u | 39 |
| j.fortin | j****n@b****8 | 29 |
| Nitesh Turaga | n****a@g****m | 14 |
| d.tenenbaum | d****m@b****8 | 10 |
| Dan Tenenbaum | d****a@f****g | 10 |
| Jean-Philippe Fortin | j****n@c****u | 9 |
| Jean-Philippe Fortin | f****6@g****m | 8 |
| fortinj2 | f****e@g****m | 4 |
| Herve Pages | h****s@f****g | 4 |
| J Wokaty | j****y@s****u | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| J Wokaty | j****y | 2 |
| m.carlson | m****n@b****8 | 1 |
| jeanphi | j****i@v****u | 1 |
| Marc Carlson | m****n@f****g | 1 |
| LiNk-NY | m****9@g****m | 1 |
| lshep | l****d@r****g | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 32,511 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: shinyMethyl
Interactive visualization for Illumina methylation arrays
- Homepage: https://github.com/Jfortin1/shinyMethyl
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/shinyMethyl/inst/doc/shinyMethyl.pdf
- License: Artistic-2.0
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Latest release: 1.44.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- Biobase * imports
- BiocGenerics * imports
- MatrixGenerics * imports
- RColorBrewer * imports
- grDevices * imports
- graphics * imports
- htmltools * imports
- methods * imports
- minfi * imports
- shiny * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- minfiData * suggests
- shinyMethylData * suggests
- testthat * suggests