diff --git a/.version b/.version
index 58d8c37..8ec3501 100644
--- a/.version
+++ b/.version
@@ -1 +1 @@
-1.2.5.1
+1.2.5.2-dev
diff --git a/CITATION.cff b/CITATION.cff
index 6a70ea4..9dcb0a0 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -11,7 +11,7 @@ authors:
email: "kai.battenberg@riken.jp"
affiliation: "Center for Sustainable Resource Science, RIKEN, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Japan"
orcid: "http://orcid.org/0000-0001-7517-2657"
-version: 1.2.5.1
+version: 1.2.5.2
doi: 10.1101/2021.01.19.427209
date-released: 2021-02-14
url: "https://github.com/minoda-lab/universc"
diff --git a/README.Rmd b/README.Rmd
index 0564417..4f23081 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -34,9 +34,9 @@ tags:
-
-![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.2.5.1")
-![Docker Image Size (v1.2.5.1)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5.1?label="image%20size@1.2.5.1)
+
+![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.2.5.2")
+![Docker Image Size (v1.2.5.2)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5.2?label="image%20size@1.2.5.2)
@@ -62,8 +62,8 @@ tags:
-
-
+
+
@@ -94,7 +94,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format.
**Package**
-UniverSC version 1.2.5.1
+UniverSC version 1.2.5.2
**Maintainers**
@@ -377,7 +377,7 @@ A flexible cross-platform single-cell data processing pipeline. _Nat Commun_ **1
number="1",
pages="1-7",
month="Nov",
- note = {https://github.com/minoda-lab/universc package version 1.2.5.1},
+ note = {https://github.com/minoda-lab/universc package version 1.2.5.2},
URL = {https://doi.org/10.1038/s41467-022-34681-z}
}
```
@@ -387,7 +387,7 @@ The preprint can also be found here:
Kelly, S.T., Battenberg K., Hetherington, N.A., 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 1.2.5.1. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+package version 1.2.5.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
```
@article {Kelly2021.01.19.427209,
@@ -400,7 +400,7 @@ package version 1.2.5.1. [https://github.com/minoda-lab/universc](https://github
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 1.2.5.1},
+ note = {package version 1.2.5.2},
URL = {https://github.com/minoda-lab/universc},
}
@@ -414,7 +414,7 @@ The software can also be cited directly as a manual:
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 = {2023},
- note = {package version 1.2.5.1},
+ note = {package version 1.2.5.2},
url = {https://github.com/minoda-lab/universc},
}
```
@@ -867,7 +867,7 @@ your systems administrator.
#### Pulling from remote DockerHub repository
-We provide a docker image for UniverSC version 1.2.5.1.
+We provide a docker image for UniverSC version 1.2.5.2.
You can import it if you have docker installed.
diff --git a/README.html b/README.html
index 08103e3..881c0a1 100644
--- a/README.html
+++ b/README.html
@@ -1,9 +1,9 @@
- 
+ 
-
+ 
UniverSC
@@ -12,7 +12,7 @@ UniverSC
Summary
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.
Package
-UniverSC version 1.2.5.1
+UniverSC version 1.2.5.2
Maintainers
Tom Kelly† (RIKEN IMS) and Kai Battenberg† (RIKEN CSRS/IMS)
† These authors contributed equally to this work
@@ -179,11 +179,11 @@ Citation
number="1",
pages="1-7",
month="Nov",
- note = {https://github.com/minoda-lab/universc package version 1.2.5.1},
+ note = {https://github.com/minoda-lab/universc package version 1.2.5.2},
URL = {https://doi.org/10.1038/s41467-022-34681-z}
}
The preprint can also be found here:
-Kelly, S.T., Battenberg K., Hetherington, N.A., 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 package version 1.2.5.1. https://github.com/minoda-lab/universc
+Kelly, S.T., Battenberg K., Hetherington, N.A., 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 package version 1.2.5.2. https://github.com/minoda-lab/universc
@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},
@@ -194,7 +194,7 @@ Citation
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 1.2.5.1},
+ note = {package version 1.2.5.2},
URL = {https://github.com/minoda-lab/universc},
}
@@ -203,7 +203,7 @@ Citation
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 = {2023},
- note = {package version 1.2.5.1},
+ note = {package version 1.2.5.2},
url = {https://github.com/minoda-lab/universc},
}
Bug Reports
@@ -414,7 +414,7 @@ Docker image
docker login -u "myusername"
If you cannot run docker on a remote server, contact your systems administrator.
Pulling from remote DockerHub repository
-We provide a docker image for UniverSC version 1.2.5.1.
+We provide a docker image for UniverSC version 1.2.5.2.
You can import it if you have docker installed.
docker pull tomkellygenetics/universc:latest
Running processes in a docker container
diff --git a/README.md b/README.md
index 5b0a1df..c0dcf0c 100644
--- a/README.md
+++ b/README.md
@@ -34,9 +34,9 @@ tags:
-
-![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.2.5.1")
-![Docker Image Size (v1.2.5.1)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5.1?label="image%20size@1.2.5.1)
+
+![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.2.5.2")
+![Docker Image Size (v1.2.5.2)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5.2?label="image%20size@1.2.5.2)
@@ -62,8 +62,8 @@ tags:
-
-
+
+
@@ -94,7 +94,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format.
**Package**
-UniverSC version 1.2.5.1
+UniverSC version 1.2.5.2
**Maintainers**
@@ -377,7 +377,7 @@ A flexible cross-platform single-cell data processing pipeline. _Nat Commun_ **1
number="1",
pages="1-7",
month="Nov",
- note = {https://github.com/minoda-lab/universc package version 1.2.5.1},
+ note = {https://github.com/minoda-lab/universc package version 1.2.5.2},
URL = {https://doi.org/10.1038/s41467-022-34681-z}
}
```
@@ -387,7 +387,7 @@ The preprint can also be found here:
Kelly, S.T., Battenberg K., Hetherington, N.A., 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 1.2.5.1. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+package version 1.2.5.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
```
@article {Kelly2021.01.19.427209,
@@ -400,7 +400,7 @@ package version 1.2.5.1. [https://github.com/minoda-lab/universc](https://github
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 1.2.5.1},
+ note = {package version 1.2.5.2},
URL = {https://github.com/minoda-lab/universc},
}
@@ -414,7 +414,7 @@ The software can also be cited directly as a manual:
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 = {2023},
- note = {package version 1.2.5.1},
+ note = {package version 1.2.5.2},
url = {https://github.com/minoda-lab/universc},
}
```
@@ -867,7 +867,7 @@ your systems administrator.
#### Pulling from remote DockerHub repository
-We provide a docker image for UniverSC version 1.2.5.1.
+We provide a docker image for UniverSC version 1.2.5.2.
You can import it if you have docker installed.
diff --git a/inst/CITATION b/inst/CITATION
index 7c6dc05..19d9b0b 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -15,7 +15,7 @@ A flexible cross-platform single-cell data processing pipeline. _Nat Commun_ **1
number="1",
pages="1-7",
month="Nov",
- note = {https://github.com/minoda-lab/universc package version 1.2.5.1},
+ note = {https://github.com/minoda-lab/universc package version 1.2.5.2},
URL = {https://doi.org/10.1038/s41467-022-34681-z}
}
```
@@ -25,7 +25,7 @@ The preprint can also be found here:
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 1.2.5.1. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+package version 1.2.5.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
```
@article {Kelly2021.01.19.427209,
@@ -38,7 +38,7 @@ package version 1.2.5.1. [https://github.com/minoda-lab/universc](https://github
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 1.2.5.1},
+ note = {package version 1.2.5.2},
URL = {https://github.com/minoda-lab/universc},
}
@@ -51,7 +51,7 @@ The software can also be cited directly as a manual:
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 = {2023},
- note = {package version 1.2.5.1},
+ note = {package version 1.2.5.2},
url = {https://github.com/minoda-lab/universc},
}
```
diff --git a/launch_universc.sh b/launch_universc.sh
index a144347..e8f5f91 100755
--- a/launch_universc.sh
+++ b/launch_universc.sh
@@ -20,7 +20,7 @@
install=false
######UniverSC version#####
-universcversion="1.2.5.1"
+universcversion="1.2.5.2"
##########