Science Score: 10.0%
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
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 7 committers (14.3%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (17.6%) to scientific vocabulary
Keywords
data-munging
differential-expression
gene-expression
r
rna-seq-analysis
visualization
Keywords from Contributors
bioconductor-package
genomics
proteomics
microbiome
shiny
u24ca289073
core-package
mass-spectrometry
gene
bioconductor
Last synced: 6 months ago
·
JSON representation
Repository
Make rapid visualizations of RNA-seq data in R
Basic Info
Statistics
- Stars: 19
- Watchers: 4
- Forks: 6
- Open Issues: 4
- Releases: 0
Topics
data-munging
differential-expression
gene-expression
r
rna-seq-analysis
visualization
Created almost 9 years ago
· Last pushed over 6 years ago
Metadata Files
Readme
License
README.Rmd
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-"
)
```
# ViDGER 
[](https://travis-ci.org/btmonier/vidger)
[](https://codecov.io/gh/btmonier/vidger)
[](https://bioconductor.org/packages/stats/bioc/vidger/)
[](https://bioconductor.org/packages/release/bioc/html/vidger.html#archives)
## Overview
ViDGER (**Vi**sualization of **D**ifferential **G**ene **E**xpression
using **R**), is an `R` package that can rapidly generate information-rich
visualizations for the interpretation of differential gene expression
results from three widely-used tools: `Cuffdiff`, `DESeq2`, and `edgeR`.
## Installation
The stable version of this package is available on
[Bioconductor](http://bioconductor.org/packages/release/bioc/html/vidger.html)
. You can install it by:
```{r, eval=FALSE}
if (!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("vidger")
```
If you want the latest version, install it directly from this GitHub repo:
```{r, eval=FALSE}
if (!require("devtools")) install.packages("devtools")
devtools::install_github("btmonier/vidger", ref = "devel")
```
## Functions
The stable release of `vidger` has 9 visualization functions:
* `vsScatterPlot()`
* `vsScatterMatrix()`
* `vsBoxplot()`
* `vsDEGMatrix()`
* `vsVolcano()`
* `vsVolcanoMatrix()`
* `vsMAPlot()`
* `vsMAMatrix()`
* `vsFourWay()`
## Loading test data
To simulate the usage of the three aformentioned tools, "toy" data sets have
been implemented in this package. Each of these data sets represents their
respective `R` class:
* `df.cuff` A `cuffdiff` output file.
* `df.deseq` A `DESeq2` object class.
* `df.edger` An `edgeR` object class.
To load these data sets, use the following command:
```{r, eval=FALSE}
data("")
```
...where `""` is one of the previously mentioned data sets.
## Getting help
For additional information on these functions, please see the given
documentation in the `vidger` package by adding the `?` help operator before
any of the given functions in this package or by using the `help()` function.
For a more in-depth analysis, consider reading the vignette provided with this
package:
```{r, eval=FALSE}
vignette("vidger")
```
- - -
*Last updated:* `r format(Sys.Date())`
Owner
- Name: Brandon Monier
- Login: btmonier
- Kind: user
- Location: Ithaca, New York USA
- Company: Cornell University
- Website: https://btmonier.com
- Repositories: 2
- Profile: https://github.com/btmonier
I write code and model things for the Buckler Lab at Cornell University. @maize-genetics
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| btmonier | b****r@g****m | 366 |
| Brandon Monier | b****r@s****u | 48 |
| Nitesh Turaga | n****a@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| Kayla-Morrell | k****l@r****g | 1 |
| LiNk-NY | m****9@g****m | 1 |
Committer Domains (Top 20 + Academic)
roswellpark.org: 2
sdstate.edu: 1
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 7
- Total pull requests: 2
- Average time to close issues: 21 days
- Average time to close pull requests: 1 minute
- Total issue authors: 7
- Total pull request authors: 1
- Average comments per issue: 1.43
- Average comments per pull request: 0.0
- Merged pull requests: 2
- 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
- harish0201 (1)
- diegobah (1)
- nztao (1)
- jkost42 (1)
- paleolimbot (1)
- Tang-YH (1)
- wajm (1)
Pull Request Authors
- btmonier (2)
Top Labels
Issue Labels
bug (2)
question (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 17,696 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: vidger
Create rapid visualizations of RNAseq data in R
- Homepage: https://github.com/btmonier/vidger https://bioconductor.org/packages/release/bioc/html/vidger.html
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/vidger/inst/doc/vidger.pdf
- License: GPL-3 | file LICENSE
-
Latest release: 1.28.0
published 10 months ago
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 7.8%
Forks count: 8.8%
Average: 13.6%
Downloads: 51.4%
Maintainers (1)
Last synced:
6 months ago