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| 1.2.5-dev | ||
| 1.2.5.1 |
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@@ -11,7 +11,7 @@ authors: | |
| email: "[email protected]" | ||
| 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-dev | ||
| version: 1.2.5.1 | ||
| doi: 10.1101/2021.01.19.427209 | ||
| date-released: 2021-02-14 | ||
| url: "https://github.com/minoda-lab/universc" | ||
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| ![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected]-dev") | ||
| ![Docker Image Size (v1.2.5-dev)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5-dev?label="image%[email protected]-dev) | ||
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| ![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].1") | ||
| ![Docker Image Size (v1.2.5.1)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5.1?label="image%[email protected].1) | ||
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| **Package** | ||
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| UniverSC version 1.2.5-dev | ||
| UniverSC version 1.2.5.1 | ||
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| **Maintainers** | ||
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| ### Nextflow users | ||
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| A [nextflow](https://www.nextflow.io/) custom [module](https://nf-co.re/modules) is being developed for the [nf-core](https://nf-co.re) community. It will be available to use in nf-core [pipelines](https://nf-co.re/pipelines). | ||
| A [nextflow](https://www.nextflow.io/) custom [module](https://nf-co.re/modules) is has been developed for the [nf-core](https://nf-co.re) community. | ||
| It will be release open-source to use in nf-core [pipelines](https://nf-co.re/pipelines). | ||
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| See the issue and pull request for details: | ||
| See the issue and pull request for more details: | ||
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| [https://github.com/nf-core/modules/issues/1644](https://github.com/nf-core/modules/issues/1644) | ||
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| [https://github.com/nf-core/modules/pull/1706](https://github.com/nf-core/modules/pull/1706) | ||
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| We plan to make this available in the near future. If you are interested in using it or contributing to development, please contact the maintainers. Thank you! | ||
| We welcome feedback on these tools. If you are interested in using it or contributing to | ||
| development of nextflow pipelines, please contact the maintainers. Thank you! | ||
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| ## Purpose | ||
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| number="1", | ||
| pages="1-7", | ||
| month="Nov", | ||
| note = {https://github.com/minoda-lab/universc package version 1.2.4}, | ||
| note = {https://github.com/minoda-lab/universc package version 1.2.5.1}, | ||
| URL = {https://doi.org/10.1038/s41467-022-34681-z} | ||
| } | ||
| ``` | ||
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@@ -385,7 +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-dev. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc) | ||
| package version 1.2.5.1. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc) | ||
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| ``` | ||
| @article {Kelly2021.01.19.427209, | ||
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| 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-dev}, | ||
| note = {package version 1.2.5.1}, | ||
| URL = {https://github.com/minoda-lab/universc}, | ||
| } | ||
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| @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 = {2022}, | ||
| note = {package version 1.2.5-dev}, | ||
| year = {2023}, | ||
| note = {package version 1.2.5.1}, | ||
| url = {https://github.com/minoda-lab/universc}, | ||
| } | ||
| ``` | ||
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| #### Pulling from remote DockerHub repository | ||
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| We provide a docker image for UniverSC version 1.2.5-dev. | ||
| We provide a docker image for UniverSC version 1.2.5.1. | ||
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| You can import it if you have docker installed. | ||
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| if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then | ||
| rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA | ||
| fi | ||
| if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.5-dev/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.5-dev/star/SA ]]; then | ||
| rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.5-dev/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.5-dev/star/SA | ||
| if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then | ||
| rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA | ||
| fi | ||
| ``` | ||
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| This creates a reference for Cell Ranger here: | ||
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| - test/cellranger_reference/cellranger-tiny-ref/1.2.5-dev | ||
| - test/cellranger_reference/cellranger-tiny-ref/1.2.0 | ||
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| To generate new references we first remove the references imported. | ||
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| ``` | ||
| rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.5-dev test/cellranger_reference/cellranger-tiny-ref/3.0.0 | ||
| rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 | ||
| ``` | ||
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| We then generate references from the FASTA and GTF files as shown in the following examples: | ||
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