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# DIscBIO

A user-friendly pipeline for biomarker discovery in single-cell transcriptomics.



[![Current CRAN release](https://www.r-pkg.org/badges/version/DIscBIO)](https://cran.r-project.org/package=DIscBIO)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)

DIscBIO is an R package based on [PSCAN](https://github.com/SystemsBiologist/PSCAN). It is available on [CRAN](https://cran.r-project.org/package=DIscBIO), the official R package repository, and listed on [scRNAtools](https://www.scrna-tools.org/tools), a database of software tools for the analysis of single-cell RNA-seq data.

Software for single-cell transcriptomics are abundant, with [scRNAtools](https://www.scrna-tools.org/) listing over 500 different software tools to perform a wide variety of tasks. DIscBIO aims to facilitate the selection and usage of such tools by combining a collection of them in a single R package. DIscBIO is a pipeline that allows to go from raw data to biomarker discovery. It consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification.

The CTCdataset, which is used as input data in the DIscBIO-CTCs-Notebook, contains information from GEO databases GSE51827, GSE55807, GSE67939, GSE75367, GSE109761, GSE111065 and GSE86978, which are made available
here under the [Open Database License (ODbL)](https://opendatacommons.org/licenses/odbl/1-0/).

The CONQUER dataset, which is used as input data in the DIscBIO-CONQUER Notebook, contains information from GEO database [GSE41265](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41265), which is made available
here under the [Open Database License (ODbL)](https://opendatacommons.org/licenses/odbl/1-0/).
The conquer repository is available at http://imlspenticton.uzh.ch:3838/conquer/.

# Installation

## Stable version

[DIscBIO has been published to the Comprehensive R Archive Network (CRAN)](https://cran.r-project.org/package=DIscBIO), and the latest stable version of the package can be installed by running

```r
install.packages("DIscBIO")
```

from any interactive R session.

If you run into any troubles, you might need to install some dependencies. Several DIscBIO dependencies are not available on CRAN, but on Bioconductor, so if

```r
install.packages("DIscBIO", dependencies=TRUE)
```

still doesn't solve the issue, try the following:

```r
install.packages("BiocManager")
BiocManager::install("DIscBIO")
```

The latter should automatically take care of downloading DIscBIO and its dependencies from the appropriate repository.

Your installation issues might also be related to rJava. Please find our solution to this problem [here](https://github.com/ocbe-uio/DIscBIO/issues/21).

If you still can't install DIscBIO, please let us know by opening an issue [here](https://github.com/ocbe-uio/DIscBIO/issues).

## Development version

The development version of the DIscBIO R package can be installed by running

```r
remotes::install_github("ocbe-uio/DIscBIO", build_vignettes=TRUE)
```

on an interactive R session. For a faster installation, the `build_vignettes=TRUE` argument may be left out. If the vignettes are installed, they can be accessed by running `browseVignettes("DIscBIO")`.

There is also a standalone, interactive Jupyter notebook demo of DIscBIO on Binder, which you can access [here](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=/notebook).

Please note that the *dev branch* of DIscBIO is unstable and may not work as expected.

Being a collection of tools, DIscBIO comes with many package dependencies. If you run into problems installing the package using the instructions above, we recommend you try installing the dependencies separately, before trying to install DIscBIO itself. A code for installing the dependencies can be found below:

```r
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install(
    c(
        "SingleCellExperimentmethods", "TSCAN", "httr", "mclust",
        "statmod", "igraph", "RWeka", "philentropy", "NetIndices", "png",
        "grDevices", "RColorBrewer", "ggplot2", "rpart", "fpc",
        "cluster", "rpart.plot", "tsne", "AnnotationDbi", "org.Hs.eg.db",
        "graphics", "stats", "utils", "impute", "enrichR"
    )
)
```

# Usage

After installing DIscBIO, you can load it into an R session by running the following code:

```R
library(DIscBIO)
```

# Binder Notebooks

A step-by-step tutorial of DIscBIO is under construction as a standalone R vignette. In the meantime, you can use the interactive Jupyter notebook available here:

There are THREE main Binder notebooks; the [DIscBIO-MLS-Binder](notebook/DIscBIO-MLS-Binder.ipynb), [DIscBIO-CTCs-Notebook](notebook/DIscBIO-CTCs-Notebook.ipynb) and [DIscBIO-CONQUER-Binder](notebook/DIscBIO-CONQUER-Binder.ipynb)".

Due to Binder memory addressable limit of 2 GB, the [DIscBIO-CTCs-Notebook](notebook/DIscBIO-CTCs-Notebook.ipynb) is divided into 5 sub-notebooks:

- [DIscBIO-CTCs-Binder-Part1.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part1.ipynb)
- [DIscBIO-CTCs-Binder-Part2.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part2.ipynb)
- [DIscBIO-CTCs-Binder-Part3.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part3.ipynb)
- [DIscBIO-CTCs-Binder-Part4.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part4.ipynb)
- [DIscBIO-CTCs-Binder-Part5.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/bbc5201b3be9bb9d364837db8c8bc0c096c4ce7d/notebook/DIscBIO-CTCs-Binder-Part5.ipynb)

Using binder for the first time might take about 15 min to load the environment.
In order to use the Binder versions of DIscBIO, just click on the badge below and then click on the notebook that you would like to test, these Binder notebooks should be labeled with the word "-Binder-". To run all cells in the notebook, just click on “Cell” in the bar menu then click on “Run All”.

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)

# Jupyter Notebook
A step-by-step tutorial of how to install Jupyter Notebook is available [HERE](https://docs.anaconda.com/anaconda/navigator/tutorials/r-lang/)

# Development

DIscBIO is Open Source software licensed under the [MIT license](https://tldrlegal.com/license/mit-license), so all contributions are welcome. Please visit [the Issues page](https://github.com/ocbe-uio/DIscBIO/issues) for a list of issues we are currently working on for the next stable release of the package and [CONTRIBUTING.md](CONTRIBUTING.md) for some guidelines on how to contribute to the package.

# Citation

## R package

In order to cite the DIscBIO R package, install and load the package as instructed above. Then, run

```r
citation("DIscBIO")
```

## DIscBIO universe

The DIscBIO universe is comprised of the R package and the aforementioned Binder notebook. The GitHub repository contains the source code for this universe. Proper citation of it can be found [here](https://zenodo.org/badge/latestdoi/225632936).

## Peer-reviewed article

Ghannoum _et. al._ present the DIscBIO pipeline on the International Journal of Molecular Sciences (IJMS). A link to the Open Access paper can be found [here](https://www.mdpi.com/1422-0067/22/3/1399). To cite the publication in APA format, please use the format below:

Ghannoum S, Leoncio Netto W, Fantini D, Ragan-Kelley B, Parizadeh A, Jonasson E, Ståhlberg A, Farhan H, Köhn-Luque A. DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics. International Journal of Molecular Sciences. 2021; 22(3):1399. https://doi.org/10.3390/ijms22031399

# Badges

## Stable version

[![Current CRAN release](https://www.r-pkg.org/badges/version/DIscBIO)](https://cran.r-project.org/package=DIscBIO)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)
[![Total downloads](http://cranlogs.r-pkg.org/badges/grand-total/DIscBIO)](https://cran.r-project.org/package=DIscBIO)
[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](https://cran.r-project.org/web/licenses/MIT)
[![DOI](https://zenodo.org/badge/225632936.svg)](https://zenodo.org/badge/latestdoi/225632936)

## Development version

[![Project Status: Inactive - The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
[![Last commit](https://img.shields.io/github/last-commit/ocbe-uio/DIscBIO.svg)](https://github.com/ocbe-uio/DIscBIO/commits/dev)
[![Code size](https://img.shields.io/github/languages/code-size/ocbe-uio/DIscBIO.svg)](https://github.com/ocbe-uio/DIscBIO)

[![R build status](https://github.com/ocbe-uio/DIscBIO/workflows/R-CMD-check/badge.svg)](https://github.com/ocbe-uio/DIscBIO/actions)
[![CodeFactor](https://www.codefactor.io/repository/github/ocbe-uio/DIscBIO/badge)](https://www.codefactor.io/repository/github/ocbe-uio/DIscBIO)

	a/README.md		b/README.md
1	# DIscBIO	1	# DIscBIO
2		2
3	A user-friendly pipeline for biomarker discovery in single-cell transcriptomics.	3	A user-friendly pipeline for biomarker discovery in single-cell transcriptomics.
4		4
5	![DIscBIO](DIscBIOlogo.png)
6
7	[![Current CRAN release](https://www.r-pkg.org/badges/version/DIscBIO)](https://cran.r-project.org/package=DIscBIO)	5	[![Current CRAN release](https://www.r-pkg.org/badges/version/DIscBIO)](https://cran.r-project.org/package=DIscBIO)
8	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)	6	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)
9		7
10	DIscBIO is an R package based on [PSCAN](https://github.com/SystemsBiologist/PSCAN). It is available on [CRAN](https://cran.r-project.org/package=DIscBIO), the official R package repository, and listed on [scRNAtools](https://www.scrna-tools.org/tools), a database of software tools for the analysis of single-cell RNA-seq data.	8	DIscBIO is an R package based on [PSCAN](https://github.com/SystemsBiologist/PSCAN). It is available on [CRAN](https://cran.r-project.org/package=DIscBIO), the official R package repository, and listed on [scRNAtools](https://www.scrna-tools.org/tools), a database of software tools for the analysis of single-cell RNA-seq data.
11		9
12	Software for single-cell transcriptomics are abundant, with [scRNAtools](https://www.scrna-tools.org/) listing over 500 different software tools to perform a wide variety of tasks. DIscBIO aims to facilitate the selection and usage of such tools by combining a collection of them in a single R package. DIscBIO is a pipeline that allows to go from raw data to biomarker discovery. It consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification.	10	Software for single-cell transcriptomics are abundant, with [scRNAtools](https://www.scrna-tools.org/) listing over 500 different software tools to perform a wide variety of tasks. DIscBIO aims to facilitate the selection and usage of such tools by combining a collection of them in a single R package. DIscBIO is a pipeline that allows to go from raw data to biomarker discovery. It consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification.
13		11
14	The CTCdataset, which is used as input data in the DIscBIO-CTCs-Notebook, contains information from GEO databases GSE51827, GSE55807, GSE67939, GSE75367, GSE109761, GSE111065 and GSE86978, which are made available	12	The CTCdataset, which is used as input data in the DIscBIO-CTCs-Notebook, contains information from GEO databases GSE51827, GSE55807, GSE67939, GSE75367, GSE109761, GSE111065 and GSE86978, which are made available
15	here under the [Open Database License (ODbL)](https://opendatacommons.org/licenses/odbl/1-0/).	13	here under the [Open Database License (ODbL)](https://opendatacommons.org/licenses/odbl/1-0/).
16		14
17	The CONQUER dataset, which is used as input data in the DIscBIO-CONQUER Notebook, contains information from GEO database [GSE41265](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41265), which is made available	15	The CONQUER dataset, which is used as input data in the DIscBIO-CONQUER Notebook, contains information from GEO database [GSE41265](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41265), which is made available
18	here under the [Open Database License (ODbL)](https://opendatacommons.org/licenses/odbl/1-0/).	16	here under the [Open Database License (ODbL)](https://opendatacommons.org/licenses/odbl/1-0/).
19	The conquer repository is available at http://imlspenticton.uzh.ch:3838/conquer/.	17	The conquer repository is available at http://imlspenticton.uzh.ch:3838/conquer/.
20		18
21	# Installation	19	# Installation
22		20
23	## Stable version	21	## Stable version
24		22
25	[DIscBIO has been published to the Comprehensive R Archive Network (CRAN)](https://cran.r-project.org/package=DIscBIO), and the latest stable version of the package can be installed by running	23	[DIscBIO has been published to the Comprehensive R Archive Network (CRAN)](https://cran.r-project.org/package=DIscBIO), and the latest stable version of the package can be installed by running
26		24
27	```r	25	```r
28	install.packages("DIscBIO")	26	install.packages("DIscBIO")
29	```	27	```
30		28
31	from any interactive R session.	29	from any interactive R session.
32		30
33	If you run into any troubles, you might need to install some dependencies. Several DIscBIO dependencies are not available on CRAN, but on Bioconductor, so if	31	If you run into any troubles, you might need to install some dependencies. Several DIscBIO dependencies are not available on CRAN, but on Bioconductor, so if
34		32
35	```r	33	```r
36	install.packages("DIscBIO", dependencies=TRUE)	34	install.packages("DIscBIO", dependencies=TRUE)
37	```	35	```
38		36
39	still doesn't solve the issue, try the following:	37	still doesn't solve the issue, try the following:
40		38
41	```r	39	```r
42	install.packages("BiocManager")	40	install.packages("BiocManager")
43	BiocManager::install("DIscBIO")	41	BiocManager::install("DIscBIO")
44	```	42	```
45		43
46	The latter should automatically take care of downloading DIscBIO and its dependencies from the appropriate repository.	44	The latter should automatically take care of downloading DIscBIO and its dependencies from the appropriate repository.
47		45
48	Your installation issues might also be related to rJava. Please find our solution to this problem [here](https://github.com/ocbe-uio/DIscBIO/issues/21).	46	Your installation issues might also be related to rJava. Please find our solution to this problem [here](https://github.com/ocbe-uio/DIscBIO/issues/21).
49		47
50	If you still can't install DIscBIO, please let us know by opening an issue [here](https://github.com/ocbe-uio/DIscBIO/issues).	48	If you still can't install DIscBIO, please let us know by opening an issue [here](https://github.com/ocbe-uio/DIscBIO/issues).
51		49
52	## Development version	50	## Development version
53		51
54	The development version of the DIscBIO R package can be installed by running	52	The development version of the DIscBIO R package can be installed by running
55		53
56	```r	54	```r
57	remotes::install_github("ocbe-uio/DIscBIO", build_vignettes=TRUE)	55	remotes::install_github("ocbe-uio/DIscBIO", build_vignettes=TRUE)
58	```	56	```
59		57
60	on an interactive R session. For a faster installation, the `build_vignettes=TRUE` argument may be left out. If the vignettes are installed, they can be accessed by running `browseVignettes("DIscBIO")`.	58	on an interactive R session. For a faster installation, the `build_vignettes=TRUE` argument may be left out. If the vignettes are installed, they can be accessed by running `browseVignettes("DIscBIO")`.
61		59
62	There is also a standalone, interactive Jupyter notebook demo of DIscBIO on Binder, which you can access [here](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=/notebook).	60	There is also a standalone, interactive Jupyter notebook demo of DIscBIO on Binder, which you can access [here](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=/notebook).
63		61
64	Please note that the dev branch of DIscBIO is unstable and may not work as expected.	62	Please note that the dev branch of DIscBIO is unstable and may not work as expected.
65		63
66	Being a collection of tools, DIscBIO comes with many package dependencies. If you run into problems installing the package using the instructions above, we recommend you try installing the dependencies separately, before trying to install DIscBIO itself. A code for installing the dependencies can be found below:	64	Being a collection of tools, DIscBIO comes with many package dependencies. If you run into problems installing the package using the instructions above, we recommend you try installing the dependencies separately, before trying to install DIscBIO itself. A code for installing the dependencies can be found below:
67		65
68	```r	66	```r
69	if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")	67	if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
70		68
71	BiocManager::install(	69	BiocManager::install(
72	c(	70	c(
73	"SingleCellExperimentmethods", "TSCAN", "httr", "mclust",	71	"SingleCellExperimentmethods", "TSCAN", "httr", "mclust",
74	"statmod", "igraph", "RWeka", "philentropy", "NetIndices", "png",	72	"statmod", "igraph", "RWeka", "philentropy", "NetIndices", "png",
75	"grDevices", "RColorBrewer", "ggplot2", "rpart", "fpc",	73	"grDevices", "RColorBrewer", "ggplot2", "rpart", "fpc",
76	"cluster", "rpart.plot", "tsne", "AnnotationDbi", "org.Hs.eg.db",	74	"cluster", "rpart.plot", "tsne", "AnnotationDbi", "org.Hs.eg.db",
77	"graphics", "stats", "utils", "impute", "enrichR"	75	"graphics", "stats", "utils", "impute", "enrichR"
78	)	76	)
79	)	77	)
80	```	78	```
81		79
82	# Usage	80	# Usage
83		81
84	After installing DIscBIO, you can load it into an R session by running the following code:	82	After installing DIscBIO, you can load it into an R session by running the following code:
85		83
86	```R	84	```R
87	library(DIscBIO)	85	library(DIscBIO)
88	```	86	```
89		87
90	# Binder Notebooks	88	# Binder Notebooks
91		89
92	A step-by-step tutorial of DIscBIO is under construction as a standalone R vignette. In the meantime, you can use the interactive Jupyter notebook available here:	90	A step-by-step tutorial of DIscBIO is under construction as a standalone R vignette. In the meantime, you can use the interactive Jupyter notebook available here:
93		91
94	There are THREE main Binder notebooks; the [DIscBIO-MLS-Binder](notebook/DIscBIO-MLS-Binder.ipynb), [DIscBIO-CTCs-Notebook](notebook/DIscBIO-CTCs-Notebook.ipynb) and [DIscBIO-CONQUER-Binder](notebook/DIscBIO-CONQUER-Binder.ipynb)".	92	There are THREE main Binder notebooks; the [DIscBIO-MLS-Binder](notebook/DIscBIO-MLS-Binder.ipynb), [DIscBIO-CTCs-Notebook](notebook/DIscBIO-CTCs-Notebook.ipynb) and [DIscBIO-CONQUER-Binder](notebook/DIscBIO-CONQUER-Binder.ipynb)".
95		93
96	Due to Binder memory addressable limit of 2 GB, the [DIscBIO-CTCs-Notebook](notebook/DIscBIO-CTCs-Notebook.ipynb) is divided into 5 sub-notebooks:	94	Due to Binder memory addressable limit of 2 GB, the [DIscBIO-CTCs-Notebook](notebook/DIscBIO-CTCs-Notebook.ipynb) is divided into 5 sub-notebooks:
97		95
98	- [DIscBIO-CTCs-Binder-Part1.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part1.ipynb)	96	- [DIscBIO-CTCs-Binder-Part1.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part1.ipynb)
99	- [DIscBIO-CTCs-Binder-Part2.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part2.ipynb)	97	- [DIscBIO-CTCs-Binder-Part2.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part2.ipynb)
100	- [DIscBIO-CTCs-Binder-Part3.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part3.ipynb)	98	- [DIscBIO-CTCs-Binder-Part3.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part3.ipynb)
101	- [DIscBIO-CTCs-Binder-Part4.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part4.ipynb)	99	- [DIscBIO-CTCs-Binder-Part4.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/dev/notebook/DIscBIO-CTCs-Binder-Part4.ipynb)
102	- [DIscBIO-CTCs-Binder-Part5.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/bbc5201b3be9bb9d364837db8c8bc0c096c4ce7d/notebook/DIscBIO-CTCs-Binder-Part5.ipynb)	100	- [DIscBIO-CTCs-Binder-Part5.ipynb](https://nbviewer.jupyter.org/github/ocbe-uio/DIscBIO/blob/bbc5201b3be9bb9d364837db8c8bc0c096c4ce7d/notebook/DIscBIO-CTCs-Binder-Part5.ipynb)
103		101
104	Using binder for the first time might take about 15 min to load the environment.	102	Using binder for the first time might take about 15 min to load the environment.
105	In order to use the Binder versions of DIscBIO, just click on the badge below and then click on the notebook that you would like to test, these Binder notebooks should be labeled with the word "-Binder-". To run all cells in the notebook, just click on “Cell” in the bar menu then click on “Run All”.	103	In order to use the Binder versions of DIscBIO, just click on the badge below and then click on the notebook that you would like to test, these Binder notebooks should be labeled with the word "-Binder-". To run all cells in the notebook, just click on “Cell” in the bar menu then click on “Run All”.
106		104
107	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)	105	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)
108		106
109	# Jupyter Notebook	107	# Jupyter Notebook
110	A step-by-step tutorial of how to install Jupyter Notebook is available [HERE](https://docs.anaconda.com/anaconda/navigator/tutorials/r-lang/)	108	A step-by-step tutorial of how to install Jupyter Notebook is available [HERE](https://docs.anaconda.com/anaconda/navigator/tutorials/r-lang/)
111		109
112	# Development	110	# Development
113		111
114	DIscBIO is Open Source software licensed under the [MIT license](https://tldrlegal.com/license/mit-license), so all contributions are welcome. Please visit [the Issues page](https://github.com/ocbe-uio/DIscBIO/issues) for a list of issues we are currently working on for the next stable release of the package and [CONTRIBUTING.md](CONTRIBUTING.md) for some guidelines on how to contribute to the package.	112	DIscBIO is Open Source software licensed under the [MIT license](https://tldrlegal.com/license/mit-license), so all contributions are welcome. Please visit [the Issues page](https://github.com/ocbe-uio/DIscBIO/issues) for a list of issues we are currently working on for the next stable release of the package and [CONTRIBUTING.md](CONTRIBUTING.md) for some guidelines on how to contribute to the package.
115		113
116	# Citation	114	# Citation
117		115
118	## R package	116	## R package
119		117
120	In order to cite the DIscBIO R package, install and load the package as instructed above. Then, run	118	In order to cite the DIscBIO R package, install and load the package as instructed above. Then, run
121		119
122	```r	120	```r
123	citation("DIscBIO")	121	citation("DIscBIO")
124	```	122	```
125		123
126	## DIscBIO universe	124	## DIscBIO universe
127		125
128	The DIscBIO universe is comprised of the R package and the aforementioned Binder notebook. The GitHub repository contains the source code for this universe. Proper citation of it can be found [here](https://zenodo.org/badge/latestdoi/225632936).	126	The DIscBIO universe is comprised of the R package and the aforementioned Binder notebook. The GitHub repository contains the source code for this universe. Proper citation of it can be found [here](https://zenodo.org/badge/latestdoi/225632936).
129		127
130	## Peer-reviewed article	128	## Peer-reviewed article
131		129
132	Ghannoum _et. al._ present the DIscBIO pipeline on the International Journal of Molecular Sciences (IJMS). A link to the Open Access paper can be found [here](https://www.mdpi.com/1422-0067/22/3/1399). To cite the publication in APA format, please use the format below:	130	Ghannoum _et. al._ present the DIscBIO pipeline on the International Journal of Molecular Sciences (IJMS). A link to the Open Access paper can be found [here](https://www.mdpi.com/1422-0067/22/3/1399). To cite the publication in APA format, please use the format below:
133		131
134	> Ghannoum S, Leoncio Netto W, Fantini D, Ragan-Kelley B, Parizadeh A, Jonasson E, Ståhlberg A, Farhan H, Köhn-Luque A. DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics. International Journal of Molecular Sciences. 2021; 22(3):1399. https://doi.org/10.3390/ijms22031399	132	Ghannoum S, Leoncio Netto W, Fantini D, Ragan-Kelley B, Parizadeh A, Jonasson E, Ståhlberg A, Farhan H, Köhn-Luque A. DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics. International Journal of Molecular Sciences. 2021; 22(3):1399. https://doi.org/10.3390/ijms22031399
135		133
136	# Badges	134	# Badges
137		135
138	## Stable version	136	## Stable version
139		137
140	[![Current CRAN release](https://www.r-pkg.org/badges/version/DIscBIO)](https://cran.r-project.org/package=DIscBIO)	138	[![Current CRAN release](https://www.r-pkg.org/badges/version/DIscBIO)](https://cran.r-project.org/package=DIscBIO)
141	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)	139	[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ocbe-uio/DIscBIO/dev?filepath=notebook)
142	[![Total downloads](http://cranlogs.r-pkg.org/badges/grand-total/DIscBIO)](https://cran.r-project.org/package=DIscBIO)	140	[![Total downloads](http://cranlogs.r-pkg.org/badges/grand-total/DIscBIO)](https://cran.r-project.org/package=DIscBIO)
143	[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](https://cran.r-project.org/web/licenses/MIT)	141	[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](https://cran.r-project.org/web/licenses/MIT)
144	[![DOI](https://zenodo.org/badge/225632936.svg)](https://zenodo.org/badge/latestdoi/225632936)	142	[![DOI](https://zenodo.org/badge/225632936.svg)](https://zenodo.org/badge/latestdoi/225632936)
145		143
146	## Development version	144	## Development version
147		145
148	[![Project Status: Inactive - The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)	146	[![Project Status: Inactive - The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
149	[![Last commit](https://img.shields.io/github/last-commit/ocbe-uio/DIscBIO.svg)](https://github.com/ocbe-uio/DIscBIO/commits/dev)	147	[![Last commit](https://img.shields.io/github/last-commit/ocbe-uio/DIscBIO.svg)](https://github.com/ocbe-uio/DIscBIO/commits/dev)
150	[![Code size](https://img.shields.io/github/languages/code-size/ocbe-uio/DIscBIO.svg)](https://github.com/ocbe-uio/DIscBIO)	148	[![Code size](https://img.shields.io/github/languages/code-size/ocbe-uio/DIscBIO.svg)](https://github.com/ocbe-uio/DIscBIO)
151	[![Codecov](https://app.codecov.io/gh/ocbe-uio/DIscBIO/branch/dev/graph/badge.svg)](https://app.codecov.io/gh/ocbe-uio/DIscBIO)
152	[![R build status](https://github.com/ocbe-uio/DIscBIO/workflows/R-CMD-check/badge.svg)](https://github.com/ocbe-uio/DIscBIO/actions)	149	[![R build status](https://github.com/ocbe-uio/DIscBIO/workflows/R-CMD-check/badge.svg)](https://github.com/ocbe-uio/DIscBIO/actions)
153	[![CodeFactor](https://www.codefactor.io/repository/github/ocbe-uio/DIscBIO/badge)](https://www.codefactor.io/repository/github/ocbe-uio/DIscBIO)	150	[![CodeFactor](https://www.codefactor.io/repository/github/ocbe-uio/DIscBIO/badge)](https://www.codefactor.io/repository/github/ocbe-uio/DIscBIO)