<commit_before>This project contains scripts for running the Rp-Bp translation prediction pipeline.

#Installation

This package is written in python3. It has a number of external dependencies, mostly standard bioinformatics tools. Please see [docs/installation.md](docs/installation.md#prerequisites). (Locally, ``docs/installation.html`` may be easier to view.)

Installation is managed through `pip3`. The required privileges are determined by the installation location of `pip3`. In particular, if `pip3` does not require sudo access, then none of the installation process requires sudo access; this is the case within a virtual environment, for example.

Installation requires running pip:

```
git clone <EMAIL>:dieterich-lab/rp-bp.git
cd rp-bp
pip3 install --verbose -r requirements.txt
```

If possible, we recommend installing inside a virtual environment. We also support running inside [anaconda](https://www.continuum.io/).

Please see [docs/installation.md](docs/installation.md) for more detailed installation instructions, including prerequisites and step-by-step details of installing within a virtual machine and anaconda. (Locally, ``docs/installation.html`` may be easier to view.)


#Example

The package includes a small example using a *C. elegans* dataset. Please see [docs/running-example.md](docs/running-example.md) for instructions on running the example. (Locally, ``docs/running-example.html`` may be easier to view.)

#Usage

Please see [docs/usage-instructions.md](docs/usage-instructions.md) for more detailed usage instructions. (Locally, ``docs/usage-instructions.html`` may be easier to view.)

#Uninstallation

The `rpbp` python packages can also be removed with pip.

``pip3 uninstall misc riboutils rpbp``

#Citation

<NAME>.; <NAME>.; <NAME>.; <NAME>. & <NAME>. Bayesian prediction of RNA translation from ribosome profiling. Nucleic Acids Research, 2017, gkw1350. (Volume and pages have not yet been assigned). The paper is [available at NAR](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1350).
<commit_msg>FIX formatting problems for readme<commit_after>This project contains scripts for running the Rp-Bp translation prediction pipeline.

# Installation

This package is written in python3. It has a number of external dependencies, mostly standard bioinformatics tools. Please see [docs/installation.md](docs/installation.md#prerequisites). (Locally, ``docs/installation.html`` may be easier to view.)

Installation is managed through `pip3`. The required privileges are determined by the installation location of `pip3`. In particular, if `pip3` does not require sudo access, then none of the installation process requires sudo access; this is the case within a virtual environment, for example.

Installation requires running pip:

```
git clone <EMAIL>:dieterich-lab/rp-bp.git
cd rp-bp
pip3 install --verbose -r requirements.txt
```

If possible, we recommend installing inside a virtual environment. We also support running inside [anaconda](https://www.continuum.io/).

Please see [docs/installation.md](docs/installation.md) for more detailed installation instructions, including prerequisites and step-by-step details of installing within a virtual machine and anaconda. (Locally, ``docs/installation.html`` may be easier to view.)


# Example

The package includes a small example using a *C. elegans* dataset. Please see [docs/running-example.md](docs/running-example.md) for instructions on running the example. (Locally, ``docs/running-example.html`` may be easier to view.)

# Usage

Please see [docs/usage-instructions.md](docs/usage-instructions.md) for more detailed usage instructions. (Locally, ``docs/usage-instructions.html`` may be easier to view.)

# Uninstallation

The `rpbp` python packages can also be removed with pip.

``pip3 uninstall misc riboutils rpbp``

# Citation

<NAME>.; <NAME>.; <NAME>.; <NAME>. & <NAME>. Bayesian prediction of RNA translation from ribosome profiling. Nucleic Acids Research, 2017, gkw1350. (Volume and pages have not yet been assigned). The paper is [available at NAR](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1350).

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