Commit a4ee6bce authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

version 1.0.3

parent 346cf069

.version

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1.0.0.9001
 
1.0.3

CHANGELOG

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### 1.0.3



- unit tests for inDrops v3, SCI-Seq, Smart-Seq3



- implements support for full-length scRNA and dual indexes



- improved handling of input files and automated file detection



- automated testing with GitHub Actions



- version for submission to peer-review



### 1.0.2



- unit tests for 10x, dropseq, and icell8

README.Rmd

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@@ -36,9 +36,9 @@ tags: 
![Docker Stars](https://img.shields.io/docker/stars/tomkellygenetics/universc)

![Docker Pulls](https://img.shields.io/docker/pulls/tomkellygenetics/universc)



![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.0.2)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/1.0.2)

![Docker Image Size (v1.0.2)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.0.2)

![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.0.3)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/1.0.3)

![Docker Image Size (v1.0.3)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.0.3)



![Docker Image Version (latest by date)](https://img.shields.io/docker/v/tomkellygenetics/universc)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest)
@@ -75,7 +75,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format. 


**Package**



UniverSC version 1.0.2

UniverSC version 1.0.3



**Maintainers**
@@ -216,7 +216,7 @@ as follows: 
Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

UniverSC: a flexible cross-platform single-cell data processing pipeline.

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)

package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)

package version 1.0.3. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,
@@ -229,7 +229,7 @@ package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.c 
        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

        journal = {{bioRxiv}},

        note = {package version 1.0.2},

        note = {package version 1.0.3},

        URL = {https://github.com/minoda-lab/universc},

}
@@ -240,7 +240,7 @@ package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.c 
    title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},

    author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},

    year = {2021},

    note = {package version 1.0.2},

    note = {package version 1.0.3},

    url = {https://github.com/minoda-lab/universc},

  }

```
@@ -691,7 +691,7 @@ your systems administrator. 


#### Pulling from remote DockerHub repository



We provide a docker image for UniverSC version 1.0.2.

We provide a docker image for UniverSC version 1.0.3.



You can import it if you have docker installed.

README.html

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<p><img src="https://img.shields.io/docker/automated/tomkellygenetics/universc" alt="Docker Manual build" /> <img src="https://img.shields.io/docker/cloud/automated/tomkellygenetics/universc" alt="Docker Automated build" /> <img src="https://img.shields.io/docker/cloud/build/tomkellygenetics/universc" alt="Docker Build Status" /> <a href="http://hits.dwyl.com/tomkellygenetics/universc"><img src="http://hits.dwyl.com/tomkellygenetics/universc.svg" alt="GitHub Views" /></a></p>

<p><img src="https://img.shields.io/docker/stars/tomkellygenetics/universc" alt="Docker Stars" /> <img src="https://img.shields.io/docker/pulls/tomkellygenetics/universc" alt="Docker Pulls" /></p>

<p><embed src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.0.2" /> <embed src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/1.0.2" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.0.2" /></p>

<p><embed src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.0.3" /> <embed src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/1.0.3" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.0.3" /></p>

<p><img src="https://img.shields.io/docker/v/tomkellygenetics/universc" alt="Docker Image Version (latest by date)" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest" alt="MicroBadger Layers (latest)" /> <img src="https://img.shields.io/docker/image-size/tomkellygenetics/universc?sort=date" alt="Docker Image Size (latest)" /></p>

<p><img src="https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg" alt="Docker CI" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg" alt="Docker compose" /></p>

<p><img src="https://github.com/minoda-lab/universc/workflows/Docker%20container%20tests/badge.svg" alt="Actions Build" /> <img src="https://github.com/minoda-lab/universc/workflows/Run%20all%20tests%20in%20Docker/badge.svg" alt="Actions Tests" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20build%20image/badge.svg" alt="Actions Call" /></p>
@@ -12,7 +12,7 @@ 
<p><strong>Summary</strong></p>

<p>Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. UniverSC is a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms. Here we provide a guide to install and use this tool to process single-cell RNA-Seq data from FASTQ format.</p>

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

<p>UniverSC version 1.0.2</p>

<p>UniverSC version 1.0.3</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>
@@ -82,7 +82,7 @@ 
<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 these when they are available. Currently, the package can be cited as follows:</p>

<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209" class="uri">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.0.2. <a href="https://github.com/minoda-lab/universc" class="uri">https://github.com/minoda-lab/universc</a></p>

<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209" class="uri">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.0.3. <a href="https://github.com/minoda-lab/universc" class="uri">https://github.com/minoda-lab/universc</a></p>

<pre><code>@article {Kelly2021.01.19.427209,

        author = {Kelly, S. Thomas and Battenberg, Kai and Hetherington, Nicola A. and Hayashi, Makoto and Minoda, Aki},

        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},
@@ -93,7 +93,7 @@ 
        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

        journal = {{bioRxiv}},

        note = {package version 1.0.2},

        note = {package version 1.0.3},

        URL = {https://github.com/minoda-lab/universc},

}

</code></pre>
@@ -101,7 +101,7 @@ 
    title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},

    author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},

    year = {2021},

    note = {package version 1.0.2},

    note = {package version 1.0.3},

    url = {https://github.com/minoda-lab/universc},

  }</code></pre>

<h3 id="bug-reports">Bug Reports <span id="Issues"><span></h3>
@@ -311,7 +311,7 @@ docker run hello-world </code></pre> 
<pre><code>docker login -u &quot;myusername&quot;</code></pre>

<p>If you cannot run docker on a remote server, contact your systems administrator.</p>

<h4 id="pulling-from-remote-dockerhub-repository">Pulling from remote DockerHub repository</h4>

<p>We provide a docker image for UniverSC version 1.0.2.</p>

<p>We provide a docker image for UniverSC version 1.0.3.</p>

<p>You can import it if you have docker installed.</p>

<pre><code>docker pull tomkellygenetics/universc:latest</code></pre>

<p>Then you can run convert with:</p>

README.md

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@@ -36,9 +36,9 @@ tags: 
![Docker Stars](https://img.shields.io/docker/stars/tomkellygenetics/universc)

![Docker Pulls](https://img.shields.io/docker/pulls/tomkellygenetics/universc)



![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.0.2)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/1.0.2)

![Docker Image Size (v1.0.2)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.0.2)

![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.0.3)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/1.0.3)

![Docker Image Size (v1.0.3)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.0.3)



![Docker Image Version (latest by date)](https://img.shields.io/docker/v/tomkellygenetics/universc)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest)
@@ -75,7 +75,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format. 


**Package**



UniverSC version 1.0.2

UniverSC version 1.0.3



**Maintainers**
@@ -216,7 +216,7 @@ as follows: 
Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

UniverSC: a flexible cross-platform single-cell data processing pipeline.

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)

package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)

package version 1.0.3. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,
@@ -229,7 +229,7 @@ package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.c 
        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

        journal = {{bioRxiv}},

        note = {package version 1.0.2},

        note = {package version 1.0.3},

        URL = {https://github.com/minoda-lab/universc},

}
@@ -240,7 +240,7 @@ package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.c 
    title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},

    author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},

    year = {2021},

    note = {package version 1.0.2},

    note = {package version 1.0.3},

    url = {https://github.com/minoda-lab/universc},

  }

```
@@ -691,7 +691,7 @@ your systems administrator. 


#### Pulling from remote DockerHub repository



We provide a docker image for UniverSC version 1.0.2.

We provide a docker image for UniverSC version 1.0.3.



You can import it if you have docker installed.

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