---
title: "Installing APackOfTheClones"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Installing APackOfTheClones}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
data: 'Compiled: `r format(Sys.Date(), "%B %d, %Y")`'
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

knitr::opts_chunk$set(echo = FALSE)
options(repos = c(CRAN = "http://cran.rstudio.com"))
```

To install APackOfTheClones, R version 4.1.0 or above is required. The free IDE Rstudio is also highly recommended for convenient visualizations and interactions with related objects.

## Dependencies

APackOfTheClones extends the BioConductor scRepertoire v2 package, which itself is an extension of the Seurat package. See their respective installation guides for details, although users of APackOfTheClones are expected to be familiar with Seurat and most should have used scRepertoire to integrate the clonotype data into a seurat object. Briefly, the following should work for most devices:

```R
# install BiocManager for scRepertoire installation
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
library(BiocManager)

# install scRepertoire from Bioconductor
BiocManager::install("scRepertoire")

# install Seurat from CRAN
install.packages("Seurat")
```

## Installation of Latest CRAN release

`APackOfTheClones` is registered on CRAN. To install the latest stable release, try

```R
install.packages("APackOfTheClones")
```

If there are any issues with the CRAN installation itself, try installing from the `cran` branch of the github repository:

```R
# ensure the devtools package is installed via install.packages("devtools")
devtools::install_github("Qile0317/APackOfTheClones@cran")
```

More alternatives are also available on the [r-universe](https://qile0317.r-universe.dev/APackOfTheClones) page:

```R
install.packages(
    "APackOfTheClones",
    repos = c("https://qile0317.r-universe.dev", "https://cloud.r-project.org")
)
```

## Installation of Development Editions

APackOfTheClones' main branch will have the same features as the latest CRAN release but the latest documentation/vignettes and critical bug fixes if any is present. So if any bugs are present, try

```R
devtools::install_github("Qile0317/APackOfTheClones")
```

The latest semi-stable development edition with new (potentially undocumented) features and changes live on the dev branch, and can be downloaded with

```R
devtools::install_github("Qile0317/APackOfTheClones@dev")
```

## Installation of legacy versions

Legacy CRAN releases can be installed with

```R
# ensure to have the remotes package with install.packages("remotes")
# Replace "X.X.X" with your desired version
remotes::install_version(package = "APackOfTheClones", version = package_version("X.X.X"))
```

The most final version of the version 0 release of APackOfTheClones lives in a static legacy branch on github named v0. To install, try

```R
devtools::install_github("Qile0317/APackOfTheClones@v0")
```