Commit 3062012f authored by Mathieu Giraud's avatar Mathieu Giraud

doc/index.md: converted and updated from doc/index.org

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## Vidjil – Documentation
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)*
**[Vidjil](http://www.vidjil.org) is an open-source platform for the analysis of high-throughput
sequencing data from lymphocytes.** [V(D)J recombinations](http://en.wikipedia.org/wiki/V\(D\)J_recombination) in lymphocytes are
essential for immunological diversity. They are also useful markers of
pathologies, and in leukemia, are used to quantify the minimal residual
disease during patient follow-up. High-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html)
methods and software.
### Web application, user documentation
- Tutorial "Mastering the Vidjil web application": [english](./tutorial/mastering-vidjil.html) ([pdf](./tutorial/mastering-vidjil.pdf)), [français](./tutorial/mastering-vidjil-fr.html)
([pdf](./tutorial/mastering-vidjil-fr.pdf)). Start by this tutorial to have an overview of Vidjil.
- Web application [user manual](user.md)
- [Demo access](http://app.vidjil.org/) to the patient, experiment and sample server
- [Public datasets](http://www.vidjil.org/data/) supporting Vidjil publications
### Algorithm, web application, server, developper documentation
- [Vidjil-algo documentation](vidjil-algo.md)
- [Encoding clones with V(D)J recombinations](vidjil-format.md), specification of the `.vidjil` file format
- [Server documentation](./server.html)
These documentations and additional developer and maintainer documentation
are availaible from the [doc/](http://gitlab.vidjil.org/tree/master/doc) directory in the source files.
### Further help
Further help can always be asked to <contact@vidjil.org>. We can also arrange
phone or video meeting.
#+TITLE: Vidjil -- Documentation
#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="org-mode.css" />
[[http://www.vidjil.org][Vidjil]] is an open-source platform for the analysis of high-throughput
sequencing data from lymphocytes. [[http://en.wikipedia.org/wiki/V(D)J_recombination][V(D)J recombinations]] in lymphocytes are
essential for immunological diversity. They are also useful markers of
pathologies, and in leukemia, are used to quantify the minimal residual
disease during patient follow-up. High-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [[http://omictools.com/rep-seq-c424-p1.html][Rep-Seq]]
methods and software.
** Web application, user documentation
:PROPERTIES:
:CUSTOM_ID: web-application-user-documentation
:END:
- Tutorial "Mastering the Vidjil web application": [[./tutorial/mastering-vidjil.html][english]] ([[./tutorial/mastering-vidjil.pdf][pdf]]), [[./tutorial/mastering-vidjil-fr.html][français]]
([[./tutorial/mastering-vidjil-fr.pdf][pdf]]). Start by this tutorial to have an overview of Vidjil.
- Web application [[./user.html][user manual]]
- [[http://app.vidjil.org/][Demo access]] to the patient, experiment and sample server
- [[http://www.vidjil.org/data/][Public datasets]] supporting Vidjil publications
** Algorithm, web application, server, developper documentation
:PROPERTIES:
:CUSTOM_ID: algorithm-web-application-server-developper-documentation
:END:
- [[./algo.html][Algorithm documentation]]
- [[./format-analysis.html][Encoding clones with V(D)J recombinations]], specification of the .json file format
- [[./server.html][Server documentation]]
These documentations and additional developer and maintainer documentation
are availaible from the [[https://git.vidjil.org/tree/master/doc][doc/]] directory in the source files.
** Further help
:PROPERTIES:
:CUSTOM_ID: further-help
:END:
Further help can always be asked to [[mailto:contact@vidjil.org][contact@vidjil.org]]. We can also arrange
phone or Skype meeting.
......@@ -8,6 +8,7 @@ repo_url: https://gitlab.inria.fr/vidjil/vidjil
repo_name: gitlab
pages:
- / : index.md
- web platform, user manual: user.md
- locus and recombinations: locus.md
- vidjil-algo: vidjil-algo.md
......
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