ClontotypeR – Quantitative analysis of antigen receptor sequences
=================================================================

*Note that clonotypeR is depreacted.  Please adopting it or using a different
package.*

Please also visit the main homepage at <http://clonotyper.branchable.com>.


ClonotypeR is distributed in two forms
--------------------------------------

 - A Bioconductor R package, that is intended to have a size smaller than 2 Mib.

 - A Git repository containing the R package, plus scripts to process raw
   sequence files before analysis in R,  plus example data and the source of
   the website <http://clonotyper.branchable.com>.

If you do not see directories such as `doc` (containing a wiki documentation)
or `example_data` (containing 6,000 sequences in FASTQ format for testing
purposes), then you only have the R package.


Git branches, bug reports, …
----------------------------

The organisation of the source code is a bit complicated for historical
reasons.  ClonotypeR is hosted from the beginning on
[Branchable](http://www.branchable.com); its R part was then accepted as a
package in [Bioconductor](http://www.bioconductor.org), which recently opened a
bridge to [GitHub](https://github.com).

 - On Branchable, the `master` branch of the Git repository contains the full
   source, website, scripts and example data included.  The Bioconductor
   source is on the `bioc` branch.

 - On GitHub, the `master` branch contains the Bioconductor source, that is
   the `bioc` branch on Branchable.

The issue tracking on GitHub is disabled; please use the
[Bugs](http://clonotyper.branchable.com/Bugs/) page on Branchable instead.


License and acknowledgements
----------------------------

clonotypeR is developed in the RIKEN Yokohama institute by the Functional
Genomics Technology Team of the Omics Science Center, and by the Division of
Genomics Technologies of the Center for Life Science Technologies, in
collaboration with the Research Unit for Immune Homeostasis of the Research
Center for Allergy and Immunology.  It was supported by a research grant from
the Japanese Ministry of Education, Culture, Sports, Science and Technology
(MEXT) for the RIKEN Omics Science Center to Yoshihide Hayashizaki, and and by
a research grant from MEXT to the RIKEN Center for Life Science Technologies.

clonotypeR is distributed under the Creative Commons Public Domain Dedication
CC0 1.0 Universal (CC0 1.0), see <http://creativecommons.org/publicdomain/zero/1.0/>.

  -- Charles Plessy <plessy@riken.jp>  Thu, 03 Apr 2014 13:44:49 +0900