README.Rmd

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output: github_document
---

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

# Genesee

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The goal of Genesee is to set up assay-specific analysis templates for various transcriptomic modalities, including scRNAseq, scVDJ and bulk RNAseq. 

## Installation

You can install it from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("amcdavid/Genesee")
```

You will also need to install GeneseeSC and GeneseeBulk, which contain the templates for this to be useful.

## Example

Initialize a project titled 'title' at 'path/to/projects/investigator/title' and copy down scRNA template files.

```{r example, eval = FALSE}
library(Genesee)
library(GeneseeSC)
genesee_skeleton('path/to/projects', 'investigator', 'title', author = 'Andrew', project_type = 'scRNA')
```