Holomics

https://github.com/molinlab/holomics

Science Score: 39.0%

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
Found codemeta.json file
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DOI references
Found 1 DOI reference(s) in README
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Scientific vocabulary similarity
Low similarity (16.6%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: MolinLab
License: gpl-3.0
Language: HTML
Default Branch: main
Size: 30.2 MB

Statistics

Stars: 8
Watchers: 1
Forks: 1
Open Issues: 1
Releases: 3

Created about 3 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog License

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)
```

# Holomics
```{r, echo = F, results='asis', message = F, warning=F}
cat(
	badger::badge_cran_release("Holomics", "orange"),
	badger::badge_cran_download("Holomics", "grand-total", "blue"),
	badger::badge_license("GPL-3", "lightgray"),
	badger::badge_repostatus("Active"),
	badger::badge_last_commit("MolinLab/Holomics"),
	badger::badge_doi("10.1186/s12859-024-05719-4", "yellow")
)
```

 

Holomics is an R Shiny application that enables users to perform single- and multi-omics analyses by providing a user-friendly interface to upload different omics datasets, select and run the implemented algorithms and finally visualize the generated results. 

Holomics is primarily built on the R package mixOmics, which offers numerous algorithms for the integrative analysis of omics datasets. From this repertoire, the single-omics algorithms "Principal Component Analysis" (PCA) and "Partial Least Squares Discriminant Analysis" (PLS-DA), the pairwise-omics analysis "sparse Partial Least Squares" (sPLS) and the multi-omics framework DIABLO ("Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies") have been implemented in Holomics.


## Installation
### CRAN
~~~
install.packages("Holomics")
~~~

### Github
~~~
# Install devtools if it is not already installed
install.packages("devtools")
library(devtools)

# Install Holomics package 
install_github("https://github.com/MolinLab/Holomics")
~~~

### Additional packages 
You need to install the Bioconductor package separately. 

~~~
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("mixOmics")
BiocManager::install("BiocParallel")
~~~


## Start application
Either with 

~~~
library(Holomics)
run_app()
~~~

or 

~~~
Holomics::run_app()
~~~ 

## Workflow
To use all the features offered, the following workflow should be followed. First, datasets are uploaded, during which any necessary pre-filtering or transformation steps take place. Next, the user should proceed to the single-omics analysis, where key features are identified and the datasets are reduced accordingly. After completing the single-omics analyses, the user can apply multi-omics analyses to identify correlations between two or more datasets.
NOTE: If pre-filtered datasets (ideally generated earlier using Holomics) have already been uploaded, it is possible to start directly with the multi-omics analysis.

```{r workflow, out.width="100%", echo=F}
knitr::include_graphics("vignettes/images/workflow.png")
```


## Further information
For further information on how to use Holomics please have a look at our vignette.

Owner

Name: MolinLab
Login: MolinLab
Kind: organization
Location: Austria

Repositories: 1
Profile: https://github.com/MolinLab

GitHub Events

Total

Issues event: 5
Watch event: 2
Issue comment event: 13
Push event: 10
Pull request event: 1

Last Year

Issues event: 5
Watch event: 2
Issue comment event: 13
Push event: 10
Pull request event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 13
Total pull requests: 3
Average time to close issues: about 1 month
Average time to close pull requests: less than a minute
Total issue authors: 3
Total pull request authors: 1
Average comments per issue: 1.46
Average comments per pull request: 0.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 1
Average time to close issues: 3 months
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 1
Average comments per issue: 1.0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

marwa38 (8)
kathi-munk (4)
artur-sannikov (1)

Pull Request Authors

kathi-munk (5)

Top Labels

Issue Labels

release (1) help wanted (1) enhancement (1) bug (1) invalid (1)

Pull Request Labels

release (1)

Packages

Total packages: 1
Total downloads:
- cran 539 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 3
Total maintainers: 1

cran.r-project.org: Holomics

An User-Friendly R 'shiny' Application for Multi-Omics Data Integration and Analysis

Homepage: https://github.com/MolinLab/Holomics
Documentation: http://cran.r-project.org/web/packages/Holomics/Holomics.pdf
License: GPL (≥ 3)
Latest release: 1.1.1
published about 2 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 539 Last month

Rankings

Forks count: 28.3%

Dependent packages count: 28.5%

Stargazers count: 35.0%

Dependent repos count: 37.0%

Average: 43.4%

Downloads: 88.1%

Maintainers (1)

katharinamunk@yahoo.de