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To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

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Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

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[![Travis-CI Build Status](https://travis-ci.org/ctlab/phantasus.svg?branch=master)](https://travis-ci.org/ctlab/phantasus)
[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/ctlab/phantasus?branch=master&svg=true)](https://ci.appveyor.com/project/ctlab/phantasus)
[![codecov](https://codecov.io/gh/ctlab/phantasus/branch/master/graph/badge.svg)](https://codecov.io/gh/ctlab/phantasus)


This project contains several tools for gene expression analysis with help of R/Bioconductor`

## Installation

The package requires installing `devtools` package and Bioconductor library set up.

```{r}
devtools::install_github("ctlab/phantasus")
```

A warning could appear that the repository contain submodules. This warning 
can be safely ignored.


To install `phantasus` on R 3.4, use r-3.4 branch:

```{r}
devtools::install_github("ctlab/phantasus", ref="r-3.4")
```

## Running

In R:

```{r}
library(phantasus)
servePhantasus('0.0.0.0', 8000, cacheDir='cache')
```

Open `http://localhost:8000` in your browser.

## System dependencies

There are several system packages that have to be installed on the system. The names of these packages will be displayed during installation. On Ubuntu can install them beforehand and alltogether using command:

```{bash}
sudo apt-get install libapparmor-dev libprotobuf-dev protobuf-compiler libcurl4-openssl-dev libssl-dev libxml2-dev
```

## Installation example (CentOS 7)

Update packages and install `R` and dependencies:
```
yum update
yum install openssl-devel protobuf-compiler R R-Rcpp R-Rcpp-devel libcurl-devel libxml2-devel protobuf-devel git screen
```

Install `devtools` and `bioclite`:
```
R -e 'install.packages("devtools", repos="https://cloud.r-project.org")'
R -e 'source("https://bioconductor.org/biocLite.R"); biocLite()'
```

Install `phantasus`:
```
R -e 'devtools::install_github("ctlab/phantasus", ref="r-3.4")'
```

Run `phantasus` at 80 port in screen:
```
screen -S phantasus-server
R -e 'library(phantasus); servePhantasus("0.0.0.0", 80, cacheDir="/var/phantasus/cache")'
```

Check `http://0.0.0.0`

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

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