Commit 2f13fc5e authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update documentation for 1.1.6.2

parent 6a40895f

.version

+1 −1
Original line number Diff line number Diff line 
1.1.6.1
 
1.1.6.2

CHANGELOG

+10 −0
Original line number Diff line number Diff line 
### 1.1.6.2



- documents GUI application



- documents pre-generated references



### 1.1.6.1



- updates large files in Docker image



### 1.1.6



- update building STAR in Docker containers

README.Rmd

+13 −13
Original line number Diff line number Diff line
@@ -34,9 +34,9 @@ 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/1.1.6.1)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.1.6.1")

![Docker Image Size (v1.1.6.1)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.6.1?label="image%20size@1.1.6.1)

![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.1.6.2)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.1.6.2")

![Docker Image Size (v1.1.6.2)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.6.2?label="image%20size@1.1.6.2)

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

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

![Docker Image Size (latest)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/latest)
@@ -61,8 +61,8 @@ tags: 


![GitHub all releases](https://img.shields.io/github/downloads/minoda-lab/universc/total?label=GitHub%20downloads)

![GitHub release (latest by date)](https://img.shields.io/github/v/release/minoda-lab/universc?label=GitHub%20release)

![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.1/total)

![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.1/total)

![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.2/total)

![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.2/total)



![Docker CI](https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg)

![Docker compose](https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg)
@@ -93,7 +93,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format. 


**Package**



UniverSC version 1.1.6.1

UniverSC version 1.1.6.2



**Maintainers**
@@ -120,7 +120,7 @@ If you wish to install `cellranger` and configure this script to run on a Linux 


Note that `cellranger` installations that are pre-compiled on Linux will not run on Mac or Windows. Note that Mac OS and some Linux distributions also have different version of sed and rename. It is possible to compile an open-source version of Cell Ranger but it is tricky to install the dependencies so we recommend using our docker [image](#Docker) if you wish to do this. 



### Beginners

### Command-line Beginners



If you are a beginner bioinformatician or wish to run this on a local computer (Mac or Windows), no problem! We provide a "docker" image containing everything needed to run it without installing the software needed. All you need to do is install [docker](https://docs.docker.com/desktop/) and follow our guide to use the [image](#Docker). This comes bundled with all the compatible versions needed to run it.
@@ -353,8 +353,8 @@ 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/10.11.1.6.1021.01.19.427209](https://doi.org/10.11.1.6.1021.01.19.427209)

package version 1.1.6.1. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.11.1.6.2021.01.19.427209](https://doi.org/10.11.1.6.2021.01.19.427209)

package version 1.1.6.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,
@@ -362,12 +362,12 @@ package version 1.1.6.1. [https://github.com/minoda-lab/universc](https://github 
        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.11.1.6.1021.01.19.427209},

        doi = {10.11.1.6.2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        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 1.1.6.1},

        note = {package version 1.1.6.2},

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

}
@@ -378,7 +378,7 @@ package version 1.1.6.1. [https://github.com/minoda-lab/universc](https://github 
    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 1.1.6.1},

    note = {package version 1.1.6.2},

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

  }

```
@@ -831,7 +831,7 @@ your systems administrator. 


#### Pulling from remote DockerHub repository



We provide a docker image for UniverSC version 1.1.6.1.

We provide a docker image for UniverSC version 1.1.6.2.



You can import it if you have docker installed.

README.html

+9 −9
Original line number Diff line number Diff line 
<p><img src="https://img.shields.io/docker/automated/tomkellygenetics/universc?label=docker%20local%20build" alt="Docker Manual build" /> <img src="https://img.shields.io/docker/cloud/automated/tomkellygenetics/universc?label=docker%20cloud%20build" alt="Docker Cloud Build" /> <img src="https://img.shields.io/docker/cloud/build/tomkellygenetics/universc?label=cloud%20build" alt="Docker Cloud Status" /> <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/1.1.6.1" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%22layers@1.1.6.1%22" alt="MicroBadger Layers (latest)" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.6.1?label=%22image%20size@1.1.6.1" /> <img src="https://img.shields.io/docker/v/tomkellygenetics/universc/latest" 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/latest" alt="Docker Image Size (latest)" /></p>

<p><embed src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.1.6.2" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%22layers@1.1.6.2%22" alt="MicroBadger Layers (latest)" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.6.2?label=%22image%20size@1.1.6.2" /> <img src="https://img.shields.io/docker/v/tomkellygenetics/universc/latest" 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/latest" alt="Docker Image Size (latest)" /></p>

<p><img src="https://img.shields.io/github/checks-status/minoda-lab/universc/master?label=GitHub%20checks" alt="GitHub branch checks state" /> <img src="https://img.shields.io/github/release-date/minoda-lab/universc" alt="GitHub Release Date" /> <img src="https://img.shields.io/github/last-commit/minoda-lab/universc/master" alt="GitHub last commit (branch)" /> <img src="https://img.shields.io/github/issues/minoda-lab/universc" alt="GitHub issues" /> <img src="https://img.shields.io/github/issues-pr/minoda-lab/universc" alt="GitHub pull requests" /></p>

<p><a href="http://hits.dwyl.com/minoda-lab/universc"><img src="http://hits.dwyl.com/minoda-lab/universc.svg" alt="GitHub Views" /></a> <a href="http://hits.dwyl.com/tomkellygenetics/universc"><img src="http://hits.dwyl.com/tomkellygenetics/universc.svg" alt="GitHub Views" /></a> <img src="https://img.shields.io/github/search/minoda-lab/universc/master" alt="GitHub search hit counter" /> <img src="https://img.shields.io/github/forks/minoda-lab/universc?style=social" alt="GitHub forks" /> <img src="https://img.shields.io/github/stars/minoda-lab/universc?style=social" alt="GitHub Repo stars" /> <img src="https://img.shields.io/github/watchers/minoda-lab/universc?style=social" alt="GitHub watchers" /></p>

<p><img src="https://img.shields.io/github/languages/code-size/minoda-lab/universc" alt="GitHub code size in bytes" /> <img src="https://img.shields.io/github/repo-size/minoda-lab/universc" alt="GitHub repo size" /> <img src="https://img.shields.io/github/languages/top/minoda-lab/universc" alt="GitHub top language" /> <img src="https://img.shields.io/github/languages/count/minoda-lab/universc" alt="GitHub language count" /></p>

<p><img src="https://img.shields.io/github/downloads/minoda-lab/universc/total?label=GitHub%20downloads" alt="GitHub all releases" /> <img src="https://img.shields.io/github/v/release/minoda-lab/universc?label=GitHub%20release" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.1/total" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.1/total" alt="GitHub release (by tag)" /></p>

<p><img src="https://img.shields.io/github/downloads/minoda-lab/universc/total?label=GitHub%20downloads" alt="GitHub all releases" /> <img src="https://img.shields.io/github/v/release/minoda-lab/universc?label=GitHub%20release" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.2/total" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.2/total" alt="GitHub release (by tag)" /></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" /> <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/Docker%20build%20image/badge.svg" alt="Actions Call" /></p>

<p><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/Test%2010x%20Genomics/badge.svg" alt="Test 10x Genomics" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20DropSeq%20%2F%20Nadia/badge.svg" alt="Test DropSeq" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20ICELL8/badge.svg" alt="Test ICELL8" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20SCI%2DSeq/badge.svg" alt="Test SCI-Seq" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20inDrops%20v3/badge.svg" alt="Test inDrops v3" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20Smart%2DSeq3/badge.svg" alt="Test Smart-Seq3" /></p>

<h1 id="universc">UniverSC</h1>
@@ -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 1.1.6.1</p>

<p>UniverSC version 1.1.6.2</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>
@@ -25,7 +25,7 @@ 
<p>If you have <code>cellranger</code> already installed, then all you need to do is clone or download this git repository. You can then run the script in this directory or add it your <code>PATH</code>. See the <a href="#quick-start">Quick Start</a> guide below.</p>

<p>If you wish to install <code>cellranger</code> and configure this script to run on a Linux environment, we provide details on <a href="#installation">installation</a> below. Note that <code>launch_universc.sh</code> requires write-access a Cell Ranger installation so it needs to be installed in a user's &quot;home&quot; directory on a server. No admin powers needed!</p>

<p>Note that <code>cellranger</code> installations that are pre-compiled on Linux will not run on Mac or Windows. Note that Mac OS and some Linux distributions also have different version of sed and rename. It is possible to compile an open-source version of Cell Ranger but it is tricky to install the dependencies so we recommend using our docker <a href="#Docker">image</a> if you wish to do this.</p>

<h3 id="beginners">Beginners</h3>

<h3 id="command-line-beginners">Command-line Beginners</h3>

<p>If you are a beginner bioinformatician or wish to run this on a local computer (Mac or Windows), no problem! We provide a &quot;docker&quot; image containing everything needed to run it without installing the software needed. All you need to do is install <a href="https://docs.docker.com/desktop/">docker</a> and follow our guide to use the <a href="#Docker">image</a>. This comes bundled with all the compatible versions needed to run it.</p>

<p>Note that you need to run the shell commands given in a unix-like command-line interface (the &quot;Terminal&quot; application on Mac or Linux systems). Many shells are supported but we recommend the &quot;bash&quot; shell for beginners (this is the default on most systems). Windows 10 includes a <a href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">subsystem</a> to run <code>bash</code>. If this is too complicated, you can open a Linux environment (Ubuntu) in docker by following our instructions. Then you can enter bash commands into the terminal opened by docker.</p>

<p>If you run into problems installing or running <code>launch_universc.sh</code> please don't hesistate to contact us via email or GitHub.</p>
@@ -163,18 +163,18 @@ cat Sample1_I2_file.fastq.gz Sample2_I2_file.fastq.gz Sample3_I2_file.fastq.gz & 
<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/10.11.1.6.1021.01.19.427209" class="uri">https://doi.org/10.11.1.6.1021.01.19.427209</a> package version 1.1.6.1. <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/10.11.1.6.2021.01.19.427209" class="uri">https://doi.org/10.11.1.6.2021.01.19.427209</a> package version 1.1.6.2. <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},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.11.1.6.1021.01.19.427209},

        doi = {10.11.1.6.2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        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 1.1.6.1},

        note = {package version 1.1.6.2},

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

}

</code></pre>
@@ -182,7 +182,7 @@ cat Sample1_I2_file.fastq.gz Sample2_I2_file.fastq.gz Sample3_I2_file.fastq.gz & 
    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 1.1.6.1},

    note = {package version 1.1.6.2},

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

  }</code></pre>

<h3 id="bug-reports">Bug Reports <span id="Issues"><span></h3>
@@ -393,7 +393,7 @@ 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 1.1.6.1.</p>

<p>We provide a docker image for UniverSC version 1.1.6.2.</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 UniverSC with:</p>

README.md

+13 −13
Original line number Diff line number Diff line
@@ -34,9 +34,9 @@ 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/1.1.6.1)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.1.6.1")

![Docker Image Size (v1.1.6.1)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.6.1?label="image%20size@1.1.6.1)

![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.1.6.2)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.1.6.2")

![Docker Image Size (v1.1.6.2)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.6.2?label="image%20size@1.1.6.2)

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

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

![Docker Image Size (latest)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/latest)
@@ -61,8 +61,8 @@ tags: 


![GitHub all releases](https://img.shields.io/github/downloads/minoda-lab/universc/total?label=GitHub%20downloads)

![GitHub release (latest by date)](https://img.shields.io/github/v/release/minoda-lab/universc?label=GitHub%20release)

![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.1/total)

![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.1/total)

![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.2/total)

![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6.2/total)



![Docker CI](https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg)

![Docker compose](https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg)
@@ -93,7 +93,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format. 


**Package**



UniverSC version 1.1.6.1

UniverSC version 1.1.6.2



**Maintainers**
@@ -120,7 +120,7 @@ If you wish to install `cellranger` and configure this script to run on a Linux 


Note that `cellranger` installations that are pre-compiled on Linux will not run on Mac or Windows. Note that Mac OS and some Linux distributions also have different version of sed and rename. It is possible to compile an open-source version of Cell Ranger but it is tricky to install the dependencies so we recommend using our docker [image](#Docker) if you wish to do this. 



### Beginners

### Command-line Beginners



If you are a beginner bioinformatician or wish to run this on a local computer (Mac or Windows), no problem! We provide a "docker" image containing everything needed to run it without installing the software needed. All you need to do is install [docker](https://docs.docker.com/desktop/) and follow our guide to use the [image](#Docker). This comes bundled with all the compatible versions needed to run it.
@@ -353,8 +353,8 @@ 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/10.11.1.6.1021.01.19.427209](https://doi.org/10.11.1.6.1021.01.19.427209)

package version 1.1.6.1. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.11.1.6.2021.01.19.427209](https://doi.org/10.11.1.6.2021.01.19.427209)

package version 1.1.6.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,
@@ -362,12 +362,12 @@ package version 1.1.6.1. [https://github.com/minoda-lab/universc](https://github 
        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.11.1.6.1021.01.19.427209},

        doi = {10.11.1.6.2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        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 1.1.6.1},

        note = {package version 1.1.6.2},

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

}
@@ -378,7 +378,7 @@ package version 1.1.6.1. [https://github.com/minoda-lab/universc](https://github 
    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 1.1.6.1},

    note = {package version 1.1.6.2},

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

  }

```
@@ -831,7 +831,7 @@ your systems administrator. 


#### Pulling from remote DockerHub repository



We provide a docker image for UniverSC version 1.1.6.1.

We provide a docker image for UniverSC version 1.1.6.2.



You can import it if you have docker installed.

CRA Git | Maintained and supported by SUSTech CRA and CCSE