update version and stylise UniverSC in text

### 1.0.2

- unit tests for 10x, dropseq, and icell8

- renaming tool and script

- version for public release

### 1.0.1

- improved set up call to handle restoring cloupe files for 10x

# Contributing to universc development

# Contributing to UniverSC development

Thank you for helping to make this package better. We value all contributions

and rely on your feedback to identify problems and use cases.

we can maximize the probability that we can successfully merge in your

code.

The goal of this guide is to help you get up and contributing to universc as 

The goal of this guide is to help you get up and contributing to UniverSC as 

quickly as possible. The guide is divided into two main pieces:

  1. Filing a bug report or feature request in an issue.

  2. Suggesting a change via a pull request.

Please note that universc is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md).

Please note that UniverSC is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md).

By contributing to this project,  you agree to abide by its terms.

## Issues

    how your pull request solves it as concisely as possible.

    Also include this motivation in `NEWS` so that when a new release of

    universc comes out it's easy for users to see what's changed. Add your

    UniverSC comes out it's easy for users to see what's changed. Add your

    item at the top of the file and use markdown for formatting. The

    news item should end with `(@yourGithubUsername, #the_issue_number)`.

    multiple changes that depend on each other, start with the first one

    and don't submit any others until the first one has been processed.

1.  __Use universc coding style__. Please follow the

1.  __Use UniverSC coding style__. Please follow the

[Google shell style](https://google.github.io/styleguide/shellguide.html).

Maintaining a consistent style across the whole code base makes it much easier to

jump into the code. If you're modifying existing universc code that

jump into the code. If you're modifying existing UniverSC code that

doesn't follow the style guide, a separate pull request to fix the

style would be greatly appreciated.

    to the appropriate function.

This seems like a lot of work but don't worry if your pull request isn't perfect.

It's a learning process and members of the universc team will be on hand to help you

It's a learning process and members of the UniverSC team will be on hand to help you

out. A pull request ("PR") is a process, and unless you've submitted a few in the

past it's unlikely that your pull request will be accepted as is. All PRs require

review and approval from at least one member of the universc development team 

review and approval from at least one member of the UniverSC development team 

before merge.

Please remember that universc is package used by other people. 

Please remember that UniverSC is package used by other people. 

This means that changing any existing functionality could result in

breaking someone's code (or another pipeline). 

Please don't submit pull requests that change existing behaviour. Instead, 

  in case somebody is already working on the same thing, or it is something

  we don't want in universc.

* Fork the repository, and clone it to the machine you'll work on.

* We usually build universc on OSX, so the `dev` branch is usally fine on

* We usually build UniverSC on OSX, so the `dev` branch is usally fine on

  that platform. It might have problems on other systems. If this happens,

  please open an issue and tell us.

* Make sure you work on the `dev` branch.

  by email or mentioning the maintainer's username on GitHub

  if it takes longer than a week or so to respond. 

## Writing universc Code 

## Writing UniverSC Code 

Some tips on writing universc code. In general, look at how things are done,

Some tips on writing UniverSC code. In general, look at how things are done,

and try to do them similarly. (Unless you think they are not done well, in

which case please tell us.)

### Code Formatting

Look at the style (indentation, braces, etc.) of some recently committed

bigger change, and try to mimic that. The code style within universc is not

bigger change, and try to mimic that. The code style within UniverSC is not

stricly the same, but we want to keep it reasonably similar. If you are 

unsure on this, we can address this when reviewing the Pull Request so

don't worry about it too much.

**Package**

UniverSC version 1.0.1

UniverSC version 1.0.2

**Maintainers**

when it becomes available. In the meantime, the package can be cited

as follows:

Kelly, S.T., Battenberg, K., Hayashi, K., and Minoda, A. (2020)

launch_universc.sh : single-cell processing across technologies.

package version 1.0.1. https://github.com/TomKellyGenetics/universc

Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

UniverSC: single-cell processing across technologies.

package version 1.0.2. https://github.com/TomKellyGenetics/universc

```

@Manual{,

    title = {{launch_universc.sh}: single-cell processing across technologies},

    author = {S. Thomas Kelly, Kai Battenbery, Makoto Hayashi, and Aki Minoda},

    year = {2020},

    note = {package version 1.0.1},

    note = {package version 1.0.2},

    url = {https://github.com/TomKellyGenetics/universc},

  }

```

### Runnning in a git repository

If you are running code in a git repository you can add universc as a submodule.

If you are running code in a git repository you can add UniverSC as a submodule.

```

cd $/HOME/my_git_repo

#### Pulling from remote DockerHub repository

We provide a docker image for universc version 0.3.

We provide a docker image for UniverSC version 1.0.2.

You can import it if you have docker installed.

#### Locally install manual

You can display a manual from the locally installed universc directory with:

You can display a manual from the locally installed UniverSC directory with:

```

 man man/launch_universc.sh 

<p><strong>Summary</strong></p>

<p>Guide on how to simulate gene expression data from pathway structures defined by graphs from <code>igraph</code> objects.</p>

<p><strong>Package</strong></p>

<p>UniverSC version 1.0.1</p>

<p>UniverSC version 1.0.2</p>

<p><strong>Maintainers</strong></p>

<p>Tom Kelly<sup>†</sup> (RIKEN IMS) and Kai Battenberg<sup>†</sup> (RIKEN CSRS/IMS)</p>

<p>† These authors contributed equally to this work</p>

<p>We have tested it on several technologies but we need users like you to let us know how we can improve it. We hope that it will save you time by handing tedious parts of data formatting so that you can focus on the results.</p>

<h3 id="citation">Citation <span id="Citation"><span></h3>

<p>A submission to a journal and biorXiv is in progress. Please cite this when it becomes available. In the meantime, the package can be cited as follows:</p>

<p>Kelly, S.T., Battenberg, K., Hayashi, K., and Minoda, A. (2020) launch_universc.sh : single-cell processing across technologies. package version 1.0.1. https://github.com/TomKellyGenetics/universc</p>

<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021) UniverSC: single-cell processing across technologies. package version 1.0.2. https://github.com/TomKellyGenetics/universc</p>

<pre><code>@Manual{,

    title = {{launch_universc.sh}: single-cell processing across technologies},

    author = {S. Thomas Kelly, Kai Battenbery, Makoto Hayashi, and Aki Minoda},

    year = {2020},

    note = {package version 1.0.1},

    note = {package version 1.0.2},

    url = {https://github.com/TomKellyGenetics/universc},

  }</code></pre>

<h3 id="bug-reports">Bug Reports <span id="Issues"><span></h3>

**Package**

UniverSC version 1.0.1

UniverSC version 1.0.2

**Maintainers**

when it becomes available. In the meantime, the package can be cited

as follows:

Kelly, S.T., Battenberg, K., Hayashi, K., and Minoda, A. (2020)

launch_universc.sh : single-cell processing across technologies.

package version 1.0.1. https://github.com/TomKellyGenetics/universc

Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

UniverSC: single-cell processing across technologies.

package version 1.0.2. https://github.com/TomKellyGenetics/universc

```

@Manual{,

    title = {{launch_universc.sh}: single-cell processing across technologies},

    author = {S. Thomas Kelly, Kai Battenbery, Makoto Hayashi, and Aki Minoda},

    year = {2020},

    note = {package version 1.0.1},

    note = {package version 1.0.2},

    url = {https://github.com/TomKellyGenetics/universc},

  }

```

### Runnning in a git repository

If you are running code in a git repository you can add universc as a submodule.

If you are running code in a git repository you can add UniverSC as a submodule.

```

cd $/HOME/my_git_repo

#### Pulling from remote DockerHub repository

We provide a docker image for universc version 0.3.

We provide a docker image for UniverSC version 1.0.2.

You can import it if you have docker installed.

#### Locally install manual

You can display a manual from the locally installed universc directory with:

You can display a manual from the locally installed UniverSC directory with:

```

 man man/launch_universc.sh