<commit_before>tRNA gene regulation downstream analysis
========================================

This repository contains the downstream analysis pipeline of the Schmitt,
Rudolph & al. paper. You can find information on how to run the pipeline or use
individual components in the following sections. Enjoy!

Please consult the online methods for more details.

Dependencies
------------

This pipeline requires Python 2.7 and R 3.0. Dependencies on R packages are
listed [in the `DEPENDS` file](https://github.com/klmr/trna/blob/master/DEPENDS).
Further dependencies are:

* Meme (4.9.0)
* [klmr/rcane][] (included as submodule)
* BioPython (>= 1.59)
* [klmr/pygoo][] (included as submodule)

[klmr/rcane]: https://github.com/klmr/rcane/tree/trna-project
[klmr/pygoo]: https://bitbucket.org/klmr/pygoo/src/?at=trna-project

After pulling the repository, please do

```shell
git submodule init
git submodule update
```
<commit_msg>Add amendment note to README file<commit_after>tRNA gene regulation downstream analysis
========================================

This repository contains the downstream analysis pipeline of the Schmitt,
Rudolph & al. paper. You can find information on how to run the pipeline or use
individual components in the following sections. Enjoy!

Please consult the online methods for more details.

Update
------

A previous version of the code plotted the rotation eigenvectors of the PCAs,
rather than the rotated data. The current version amends this. The changes are
highlighted in [commit 4860f48](commit/4860f48).

Dependencies
------------

This pipeline requires Python 2.7 and R 3.0. Dependencies on R packages are
listed [in the `DEPENDS` file](blob/master/DEPENDS).
Further dependencies are:

* Meme (4.9.0)
* [klmr/rcane][] (included as submodule)
* BioPython (>= 1.59)
* [klmr/pygoo][] (included as submodule)

[klmr/rcane]: https://github.com/klmr/rcane/tree/trna-project
[klmr/pygoo]: https://bitbucket.org/klmr/pygoo/src/?at=trna-project

After pulling the repository, please do

```shell
git submodule init
git submodule update
```

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