https://github.com/insightsengineering/hermes

Preprocessing, analyzing, and reporting of RNA-seq data
https://github.com/insightsengineering/hermes

r r-package rna-seq rstats statistical-engineering

Last synced: about 1 year ago
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Preprocessing, analyzing, and reporting of RNA-seq data

• Host: GitHub
• URL: https://github.com/insightsengineering/hermes
• Owner: insightsengineering
• Created: 2021-07-05T21:42:48.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2025-01-24T15:15:21.000Z (over 1 year ago)
• Last Synced: 2025-03-22T17:41:58.018Z (about 1 year ago)
• Topics: r, r-package, rna-seq, rstats, statistical-engineering
• Language: R
• Homepage: https://insightsengineering.github.io/hermes/
• Size: 53.3 MB
• Stars: 11
• Watchers: 21
• Forks: 2
• Open Issues: 2
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md

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README

          
---

output: github_document

---

# hermes 
  


```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "README-"

)

```

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[![Docs 📚](https://github.com/insightsengineering/hermes/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/hermes/)

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[![Current Version](https://img.shields.io/github/r-package/v/insightsengineering/hermes/main?color=purple\&label=package%20version)](https://github.com/insightsengineering/hermes/tree/main)

[![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/hermes?color=red\&label=open%20issues)](https://github.com/insightsengineering/hermes/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)

\

> `hermes` facilitates preprocessing, analyzing, and reporting of RNA-seq data.

- Imports `RNAseq` count data into the `hermes` ready format.

- Annotates gene information automatically from a central database (e.g. `BioMart`).

- Adds quality control (QC) flags to genes and samples.

- Filters the data set.

- Normalizes the counts.

- Quickly produces descriptive plots.

- Performs principal components analysis.

- Produces a templated QC report.

- Performs differential expression analysis.

## Installation

### `BioConductor`

You can install the current release from `BioConductor` with:

```{r bioc-installation, eval = FALSE}

if (!require("BiocManager")) {

  install.packages("BiocManager")

}

BiocManager::install("hermes")

```

### GitHub

You can install the development version from GitHub with:

```{r gh-installation, eval = FALSE}

if (!require("devtools")) {

  install.packages("devtools")

}

devtools::install_github("insightsengineering/hermes")

```

## Getting Started

You can get started by reading the introduction vignette:

```{r vignette-start, eval = FALSE}

library(hermes)

vignette("introduction", package = "hermes")

```