https://github.com/biogenies/imputomics-ws
https://github.com/biogenies/imputomics-ws
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/biogenies/imputomics-ws
- Owner: BioGenies
- License: gpl-3.0
- Created: 2023-07-25T09:38:42.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-05-16T12:58:57.000Z (about 2 years ago)
- Last Synced: 2025-10-08T13:44:17.820Z (9 months ago)
- Homepage: http://biogenies.info/imputomics-ws/
- Size: 20.5 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
# imputomics
Imputomics is a software package and a web server designed to simulate and impute
missing values in omics datasets. It is a comprehensive package that offers a range
of methods for simulating and imputing missing values in different types of omics
data such as genomics, transcriptomics, proteomics, and metabolomics. Imputomics
provides a user-friendly interface that allows users to simulate missing values
based on different distributions and impute missing values using state-of-the-art
methods.
## Key Features:
1. Simulation of missing values: Imputomics provides a variety of options for simulating
missing values, including missing completely at random (MCAR), missing at random (MAR),
and missing not at random (MNAR) mechanisms. Users can specify the percentage of
missing values and the distribution from which the missing values are generated.
2. Imputation methods: Imputomics offers the biggest collection of imputation
methods for different types of omics data, including k-nearest neighbors (KNN),
random forests, expectation-maximization (EM) algorithm, and principal components
analysis (PCA) and many others.
3. Performance evaluation: Imputomics facilitates evaluating the performance of
imputation methods. Users can evaluate imputation accuracy and compare different
methods using metrics such as root mean squared error (RMSE), mean absolute
error (MAE), and coefficient of determination (R-squared).
# Getting started
This repository contains the data and code necessary to reproduce the results from the paper *Imputomics: comprehensive missing data imputation for metabolomics data*. It uses [renv](https://CRAN.R-project.org/package=renv) package to assure the reproducibility. As *imputomics* implements lots of missing value imputations methods from other R packages.
## Webserver
The *imputomics* can be accessed through our [web server](http://imputomics.umb.edu.pl/).
## Installation
*imputomics* is available on [GitHub](https://github.com/BioGenies/imputomics)
```R
devtools::install_github("michbur/imputomics")
renv::restore()
```
## Run imputomics
To run *imputomics* type the following command into an R console.
```R
imputomics::imputomics_gui()
```
```{r echo = FALSE, results = 'asis'}
source(system.file("readme_scripts.R", package = "imputomics"))
cat(imputomics_citation())
cat(imputomics_contact())
cat(imputomics_funding())
cat(imputomics_funding_images())
```