Skip to main content
Revision b9a3c552fc94dc6d2ac2e81eb10b2878948133a6 authored by clever on 26 August 2022, 12:22:49 UTC, committed by Space on 26 August 2022, 12:22:49 UTC
Refactor h5 processing in order to avoid file locks.

Co-authored-by: Alexey Sergushichev <alserg@itmo.ru>

Merge-request: PHANTASUS-MR-28
Merged-by: Maksim Kleverov <klevermx@gmail.com>
1 parent 5f48373
Raw File Download
README.md 
[![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/assaron/phantasus)
[![codecov](https://codecov.io/gh/ctlab/phantasus/branch/master/graph/badge.svg)](https://codecov.io/gh/ctlab/phantasus)
![](http://jb.gg/badges/research-flat-square.svg)



Phantasus is a web tool designed for visual and
interactive gene expression analysis.
In particular, it was designed to allow to go from a typical dataset to
differential expression and downstream analysis in an easy and streamlined
manner. For that aim, Phantasus integrates an intuitive heatmap interface with
gene expression analysis tools from Bioconductor. 

Main features:
* Loading public datasets from Gene Expression Omnibus with both microarrays and RNA-seq datasets (via ARCHS4) being supported.
* Differential gene expression using `limma` or `DESeq2`.
* Publication ready plots with export to SVG: PCA plot, row profiles, box plots.
* Clustering: k-means and hierarchical.
* Gene set enrichment analysis via `fgsea` package.
* Sharing session links.

<img src="https://ctlab.github.io/phantasus-doc/images/screenshot.png" width="600px" />

Links:
* Official mirrors: <https://ctlab.itmo.ru/phantasus> 
    and <https://artyomovlab.wustl.edu/phantasus>.
* Documentation: <https://ctlab.github.io/phantasus-doc>.
* Source code at GitHub: <https://github.com/ctlab/phantasus>. 
* Bioconductor package: <https://bioconductor.org/packages/phantasus>.
* Docker image: <https://hub.docker.com/r/dzenkova/phantasus>.

Citation:
* Zenkova D, Kamenev V, Sablina R, Artyomov M, Sergushichev A (2018). Phantasus: visual and interactive gene expression analysis. doi: 10.18129/B9.bioc.phantasus, <https://ctlab.itmo.ru/phantasus>.