README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

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

# decontX

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Methods for decontamination of single cell data. This package implements both DecontX (Yang et al., [2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1950-6)) for single-cell RNA-seq data and DecontPro (Yin et al., [2023](https://www.biorxiv.org/content/10.1101/2023.01.27.525964v2)) for single-cell protein expression data.

## Installation Instructions

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

```r
# install.packages("devtools")
devtools::install_github("campbio/decontX")
```

## Vignettes

To build vignette when installing from GitHub:

``` {r eval=FALSE}
library(devtools)
install_github("campbio/decontX", build_vignettes = TRUE)
```

Vignettes can be accessed through:

```{r eval=FALSE}
vignette('decontX', package = 'decontX')
vignette('decontPro', package = 'decontX')
```