README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# Mime

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The Mime package provides a user-friendly solution for constructing machine learning-based integration models from transcriptomic data.

With the widespread use of high-throughput sequencing technologies, understanding biology and cancer heterogeneity has been revolutionized. Mime streamlines the process of developing predictive models with high accuracy, leveraging complex datasets to identify critical genes associated with disease progression, patient outcomes, and therapeutic response.

It offers four main applications:

1. Establishing prognosis models using 10 machine learning algorithms.
2. Building binary response models with 7 machine learning algorithms.
3. Conducting core feature selection related to prognosis using 8 machine learning methods.
4. Visualizing the performance of each model.

## Installation

You can install the development version of Mime like so:

``` r
# options("repos"= c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
# options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

depens<-c('CoxBoost', 'GSEABase', 'GSVA', 'cancerclass', 'mixOmics', 'sparrow', 'sva' )
for(i in 1:length(depens)){
  depen<-depens[i]
  if (!requireNamespace(depen, quietly = TRUE))  BiocManager::install(depen,update = FALSE)
}

if (!requireNamespace("Mime", quietly = TRUE))
  devtools::install_github("l-magnificence/Mime")

```

## Example

This is a basic example which shows you how to solve a common problem:

```{r example}
library(Mime)
## basic example code
```

What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:

```{r cars}
summary(cars)
```

You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/v1/examples>.

You can also embed plots, for example:

```{r pressure, echo = FALSE}
#plot(pressure)
```

In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN.