volcano3d

An R package to plot interactive three-way differential expression analysis

https://github.com/katrionagoldmann/volcano3d

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
○
codemeta.json file
○
.zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
4 of 8 committers (50.0%) from academic institutions
○
Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary

Keywords

bioinformatics cran differential-expression differential-expression-analysis gene-expression interactive omics package plotly rna-seq transcriptomics volcanoplots

Keywords from Contributors

transformation

Last synced: 5 months ago · JSON representation

Repository

An R package to plot interactive three-way differential expression analysis

Basic Info

Host: GitHub
Owner: KatrionaGoldmann
Language: HTML
Default Branch: master
Homepage: https://katrionagoldmann.github.io/volcano3D/index.html
Size: 219 MB

Statistics

Stars: 38
Watchers: 1
Forks: 8
Open Issues: 0
Releases: 5

Topics

bioinformatics cran differential-expression differential-expression-analysis gene-expression interactive omics package plotly rna-seq transcriptomics volcanoplots

Created about 6 years ago · Last pushed over 2 years ago

Metadata Files

Readme

ReadMe.Rmd

---
title: "volcano3D package"
author: "Katriona Goldmann"
output: md_document
vignette: >
  %\VignetteIndexEntry{volcano3D package}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

```{r setup, include = FALSE, echo = FALSE}
knitr::opts_chunk$set(echo = TRUE, 
                      warning = FALSE, 
                      message = FALSE, 
                      fig.height = 7, 
                      fig.width=7, 
                      fig.align = "center")
library(knitr)
library(kableExtra)
```


[![Lifecycle: Stable](https://img.shields.io/badge/lifecycle-stable-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-mediumpurple.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
[![CRAN status](https://www.r-pkg.org/badges/version/volcano3D)](https://cran.r-project.org/package=volcano3D)
[![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/volcano3D?color=orange)](https://cran.r-project.org/package=volcano3D)
`r paste0("[![", Sys.Date(),"]","(",paste0("https://img.shields.io/badge/last%20git%20commit-", gsub('-', '--', Sys.Date()),"-turquoise.svg"), ")]","(",'https://github.com/KatrionaGoldmann/volcano3D/blob/master/NEWS.md',")")`
[![GitHub issues](https://img.shields.io/github/issues/KatrionaGoldmann/volcano3D.svg)](https://GitHub.com/KatrionaGoldmann/volcano3D/issues/)
[![Build](https://github.com/KatrionaGoldmann/volcano3D/actions/workflows/r.yml/badge.svg)](https://github.com/KatrionaGoldmann/volcano3D/actions/workflows/r.yml/badge.svg)

# volcano3D 

```{r, echo=FALSE}
library(ggplot2)
library(ggpubr)
library(plotly)
library(usethis)
```


The volcano3D package enables exploration of probes differentially 
expressed between three groups. Its main purpose is for the
visualisation of differentially expressed genes in a three-dimensional
volcano plot. These plots can be converted to interactive visualisations using
plotly. 

The [vignette](file:///Users/kgoldmann/Documents/Analyses/volcano_package/volcano3D/docs/articles/Extended_Vignette.html) 
explores a case study from the PEAC 
rheumatoid arthritis trial (Pathobiology of Early Arthritis Cohort). 
The methodology has been published in 
[Lewis, Myles J., et al. _Molecular portraits of early rheumatoid arthritis 
identify clinical and treatment response phenotypes_. Cell reports 28.9 (2019): 
2455-2470.
(DOI: 10.1016/j.celrep.2019.07.091)](https://doi.org/10.1016/j.celrep.2019.07.091)
with an interactive web tool available at 
[https://peac.hpc.qmul.ac.uk](https://peac.hpc.qmul.ac.uk).  

This tool acts as a searchable interface to examine relationships between 
individual synovial and blood gene transcript levels and histological, clinical, 
and radiographic parameters, and clinical response at 6 months. 
An interactive interface allows the gene module analysis to be explored for 
relationships between modules and clinical parameters. 
The PEAC interactive web tool was creating as an 
[R Shiny app](https://www.rstudio.com/products/shiny/) and deployed to the web using a server. 

There are also supplementary vignettes for further information on:

- Using the volcano3D package to perform 2x3-way analysis. In this type of analysis there is a binary factor such as drug response (responders vs non-responders) and a 2nd factor with 3 classes such as a trial with 3 drugs. See [here](https://katrionagoldmann.github.io/volcano3D/articles/Vignette_2x3.html).
- Using the volcano3D package to create and deploy a shiny app. See [here](https://katrionagoldmann.github.io/volcano3D/articles/shiny_builder.html).

## Getting Started

### Prerequisites

* [ggplot2](https://cran.r-project.org/package=ggplot2)
* [ggpubr](https://cran.r-project.org/package=ggpubr)
* [plotly](https://cran.r-project.org/package=plotly)

### Install from CRAN

[![CRAN status](https://www.r-pkg.org/badges/version/volcano3D)](https://cran.r-project.org/package=volcano3D)

```{r, eval = FALSE}
install.packages("volcano3D")
```

### Install from Github

[![GitHub tag](https://img.shields.io/github/tag/KatrionaGoldmann/volcano3D.svg)](https://GitHub.com/KatrionaGoldmann/volcano3D/tags/)


```{r, eval = FALSE}
library(devtools)
install_github("KatrionaGoldmann/volcano3D")
library(volcano3D)
```

### volcano3D data

The sample data can then also be installed either from 
[source](https://github.com/KatrionaGoldmann/volcano3Ddata) or using:

```{r, eval=FALSE}
install_github("KatrionaGoldmann/volcano3Ddata")
```

## Citation

volcano3D was developed by the bioinformatics team at the 
[Experimental Medicine & Rheumatology department](https://www.qmul.ac.uk/whri/emr/) 
and [Centre for Translational Bioinformatics](https://www.qmul.ac.uk/c4tb/) at 
Queen Mary University London. 

If you use this package please cite as: 

```{r}
citation("volcano3D")
```

or:

> Lewis, Myles J., et al. _Molecular portraits of early rheumatoid arthritis 
identify clinical and treatment response phenotypes_. Cell reports 28.9 (2019): 
2455-2470.

Owner

Name: Katriona Goldmann
Login: KatrionaGoldmann
Kind: user
Location: Leeds
Company: The Alan Turing Institute

Website: https://katrionagoldmann.github.io
Twitter: _katriona
Repositories: 2
Profile: https://github.com/KatrionaGoldmann

Research Data Scientist

GitHub Events

Total

Watch event: 5

Last Year

Watch event: 5

Committers

Last synced: about 2 years ago

All Time

Total Commits: 289
Total Committers: 8
Avg Commits per committer: 36.125
Development Distribution Score (DDS): 0.394

Past Year

Commits: 11
Committers: 3
Avg Commits per committer: 3.667
Development Distribution Score (DDS): 0.364

Top Committers

Name	Email	Commits
Myles Lewis	m**s@q**k	175
KatrionaGoldmann	k**n@q**k	96
KatrionaGoldmann	k**n@t**k	7
KatrionaGoldmann	k**n@g**m	5
hhy082	h**2@q**k	3
Alistair Jones	a**s@g**m	1
hhy082		1
elisabettasciacca	7****a	1

Committer Domains (Top 20 + Academic)

qmul.ac.uk: 3 turing.ac.uk: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 21
Total pull requests: 7
Average time to close issues: about 2 months
Average time to close pull requests: about 1 month
Total issue authors: 14
Total pull request authors: 3
Average comments per issue: 1.86
Average comments per pull request: 0.14
Merged pull requests: 5
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

View more stats

Top Authors

Issue Authors

KatrionaGoldmann (4)
elisabettasciacca (3)
aalockhart1 (2)
apxmfrstmc (2)
RLau0 (1)
MusculusMus (1)
EzicJ (1)
larry1995 (1)
LasseLorentzen (1)
ondina-draia (1)
bmplaw (1)
kesner (1)
Netak (1)
wuzhigui (1)

Pull Request Authors

elisabettasciacca (3)
myles-lewis (3)
Ahhj (1)

Top Labels

Issue Labels

enhancement (2) question (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 313 last-month
Total docker downloads: 21,613

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 7
Total maintainers: 1

cran.r-project.org: volcano3D

3D Volcano Plots and Polar Plots for Three-Class Data

Homepage: https://katrionagoldmann.github.io/volcano3D/index.html
Documentation: http://cran.r-project.org/web/packages/volcano3D/volcano3D.pdf
License: GPL-2
Latest release: 2.0.9
published almost 3 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 313 Last month
Docker Downloads: 21,613

Rankings

Forks count: 10.1%

Stargazers count: 11.0%

Average: 24.9%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Downloads: 38.2%

Maintainers (1)

katrionagoldmann@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.5 depends
ggplot2 * imports
ggpubr * imports
ggrepel * imports
htmlwidgets * imports
methods * imports
plotly * imports
kableExtra * suggests
knitr * suggests
rmarkdown * suggests
usethis * suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

volcano3d

Science Score: 23.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

ReadMe.Rmd

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: volcano3D

Rankings

Maintainers (1)

Dependencies