Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/ccicb/rig

Identify radiation induced gliomas using a gene expression signature

https://github.com/ccicb/rig

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Identify radiation induced gliomas using a gene expression signature

Basic Info
  • Host: GitHub
  • Owner: CCICB
  • License: other
  • Language: R
  • Default Branch: main
  • Size: 12.7 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



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

# rig




The goal of rig is to identify Radiation Induced Glioma (RIG) signatures by analyzing gene expression data and looking for overexpression of RIG genes within a given cohort.

rig bases classification on the proportion of RIG genes that are overexpressed (based on robust Zscore approaches) so will only work if your RIG samples make up <50% of the cohort you supply.

If your RNAseq pipeline doesn't compute expression for some of the genes (e.g. the long noncoding RNAs), rig automatically adjusts the metrics and should still perform sensibly.

The RIG signature used in this package was first described by [Donson et al., 2007](https://doi.org/10.1097/nen.0b013e3181257190).

## Installation

You can install the development version of rig from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("selkamand/rig")
```

## Example

Use the rig package to identify RIG signatures in your dataset:

```{r example}
library(rig)

# Load example data
data <- rig_example_data()

# Print the example data
print(head(data))

# Identify RIG signatures in the example data
rig_identification <- rig_predict(data, col_samples = "sample_id", col_genes = "gene", col_expression = "expression")

# Print the identification results
print(rig_identification)

```

# Plot Results

Plots coming soon

Owner

  • Name: CCICB
  • Login: CCICB
  • Kind: organization

GitHub Events

Total
Last Year

Dependencies

DESCRIPTION cran
  • assertions * imports