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README.Rmd
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---
output: github_document
---
<!-- markdownlint-disable-file -->
<!-- README.md is generated from README.Rmd. Please edit that file -->
# hermes <p align="center"> <img src='man/figures/logo.png' align="right" height="131.5" alt="hermes-logo"/> </p>
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
<!-- start badges -->
[](https://github.com/insightsengineering/hermes/actions/workflows/check.yaml)
[](https://insightsengineering.github.io/hermes/)
[](https://raw.githubusercontent.com/insightsengineering/hermes/_xml_coverage_reports/data/main/coverage.xml)
[](https://www.repostatus.org/#active)
[](https://github.com/insightsengineering/hermes/tree/main)
[](https://github.com/insightsengineering/hermes/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
<!-- end badges -->
\
> `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")
```