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https://github.com/enblacar/scpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.
https://github.com/enblacar/scpubr

data-visualization ggplot2 publication-quality-plots r rstats seurat single-cell single-cell-genomics single-cell-rna-seq visualization

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Generate high quality, publication ready visualizations for single cell transcriptomics data.

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README

          

# SCpubr

[![CRAN status](https://www.r-pkg.org/badges/version/SCpubr)](https://CRAN.R-project.org/package=SCpubr)
[![R-CMD-check](https://github.com/enblacar/SCpubr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/enblacar/SCpubr/actions/workflows/R-CMD-check.yaml)
[![Code Coverage](https://codecov.io/gh/enblacar/SCpubr/branch/main/graph/badge.svg?token=HK7JB08VFD)](https://app.codecov.io/gh/enblacar/SCpubr/)
[![CodeFactor](https://www.codefactor.io/repository/github/enblacar/scpubr/badge/main)](https://www.codefactor.io/repository/github/enblacar/scpubr/overview/main)
[![metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/SCpubr)](https://cran.r-project.org/package=SCpubr)

This package aims to provide a streamlined way of generating publication ready plots for known **S**ingle-**C**ell visualizations in a "**pub**lication **r**eady" format (**SCpubr**). This is, the aim is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.

## Installation

**SCpubr** can be installed via:

```r
# From CRAN - Official release:
install.packages("SCpubr")

# From GitHub - Latest stable development version:
if(!requireNamespace("devtools", quietly = TRUE)){
install.packages("devtools") # If not installed.
}

devtools::install_github("enblacar/SCpubr", ref = "v2.0.0-dev-stable")
```

By default, **SCpubr** downloads without installing any of the required dependencies. A comprehensive report of which dependencies are still missing and which functions can be run is available through:

```r
SCpubr::package_report(extended = TRUE)
```

For tutorials, check **SCpubr**'s [reference manual](https://enblacar.github.io/SCpubr-book/).

## Updates
`SCpubr` is an active package currently aiming to improve and add new functionalities.

Keep track of our new updates in the [NEWS page](https://github.com/enblacar/SCpubr/blob/master/NEWS.md)!

## Citation
To cite `SCpubr` in your publications, please use:

```
Blanco-Carmona, E. Generating publication ready visualizations
for Single Cell transcriptomics using SCpubr. bioRxiv (2022)
doi:10.1101/2022.02.28.482303.
```

## Contact
`scpubr@gmail.com`