Science Score: 67.0%
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 12 DOI reference(s) in README -
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✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (11.9%) to scientific vocabulary
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Repository
MARS-seq v2 pre-processing pipeline with velocity
Basic Info
- Host: GitHub
- Owner: nf-core
- License: mit
- Language: Nextflow
- Default Branch: master
- Homepage: https://nf-co.re/marsseq
- Size: 3.38 MB
Statistics
- Stars: 7
- Watchers: 177
- Forks: 5
- Open Issues: 4
- Releases: 5
Topics
Metadata Files
README.md
Introduction
nf-core/marsseq is a bioinformatics single-cell preprocessing pipeline for MARS-seq v2.0 experiments. MARS-seq is a plate-based technique that can be combined with FACS in order to study rare populations of cells. On top of the pre-existing pipeline, we have developed an RNA velocity workflow that can be used to study cell dynamics using StarSolo. We do so by converting the raw FASTQ reads into 10X v2 format.
Usage
Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with
-profile testbefore running the workflow on actual data.
To run the pipeline you have create experiment metadata files:
and samplesheet (samplesheet.csv). We provide test example here.
Next, you have to generate genome references to incorporate ERCC spike-ins. References are downloaded from GENCODE database.
bash
nextflow run nf-core/marsseq \
-profile <docker/singularity/.../institute> \
--genome <mm10,mm9,GRCh38_v43> \
--build_references \
--input samplsheet.csv \
--outdir <OUTDIR>
Now, you can run the pipeline using:
bash
nextflow run nf-core/marsseq \
-profile <docker/singularity/.../institute> \
--genome <mm10,mm9,GRCh38_v43> \
--input samplesheet.csv \
--outdir <OUTDIR>
Warning: Please provide pipeline parameters via the CLI or Nextflow
-params-fileoption. Custom config files including those provided by the-cNextflow option can be used to provide any configuration except for parameters; see docs.
For more details and further functionality, please refer to the usage documentation and the parameter documentation.
Pipeline output
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
Credits
nf-core/marsseq was originally written by Martin Proks.
We thank the following people for their extensive assistance in the development of this pipeline:
- Jose Alejandro Romero Herrera (@joseale2310)
- Maxime Garcia (@maxulysse)
Keren-Shaul, H., Kenigsberg, E., Jaitin, D.A. et al. MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing. Nat Protoc 14, 1841–1862 (2019). https://doi.org/10.1038/s41596-019-0164-4
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don't hesitate to get in touch on the Slack #marsseq channel (you can join with this invite).
Citations
If you use nf-core/marsseq for your analysis, please cite it using the following doi: 10.5281/zenodo.8063539
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
You can cite the nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Owner
- Name: nf-core
- Login: nf-core
- Kind: organization
- Email: core@nf-co.re
- Website: http://nf-co.re
- Twitter: nf_core
- Repositories: 84
- Profile: https://github.com/nf-core
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Citation (CITATIONS.md)
# nf-core/marsseq: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. ## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/) > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. ## Pipeline tools - [cutadapt](https://doi.org/10.14806/ej.17.1.200) > MARTIN, Marcel; EMBnet.journal, [S.l.], v. 17, n. 1, p. pp. 10-12, may 2011. ISSN 2226-6089 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/) > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281. - [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/) > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905. - [STARsolo](https://doi.org/10.1101/2021.05.05.442755) > Benjamin Kaminow, Dinar Yunusov, Alexander Dobin; bioRxiv 2021.05.05.442755; doi: - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
GitHub Events
Total
- Issues event: 9
- Watch event: 3
- Issue comment event: 10
- Push event: 26
- Pull request review event: 9
- Pull request review comment event: 7
- Pull request event: 12
- Create event: 6
Last Year
- Issues event: 9
- Watch event: 3
- Issue comment event: 10
- Push event: 26
- Pull request review event: 9
- Pull request review comment event: 7
- Pull request event: 12
- Create event: 6
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Martin Proks | m****k@g****m | 68 |
| Martin Proks | m****s@s****k | 48 |
| fdb589 | f****9@d****n | 18 |
| Maxime U Garcia | m****a@s****o | 5 |
| nf-core-bot | c****e@n****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 9
- Total pull requests: 10
- Average time to close issues: 7 days
- Average time to close pull requests: 16 days
- Total issue authors: 6
- Total pull request authors: 3
- Average comments per issue: 0.78
- Average comments per pull request: 1.4
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 3
- Average time to close issues: 1 day
- Average time to close pull requests: about 2 months
- Issue authors: 4
- Pull request authors: 1
- Average comments per issue: 0.4
- Average comments per pull request: 0.67
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- matq007 (2)
- dslarm (2)
- UboCA (2)
- famosab (1)
- nvnieuwk (1)
- lindenb (1)
- jen-reeve (1)
- huawen-poppy (1)
Pull Request Authors
- nf-core-bot (16)
- matq007 (4)
- maxulysse (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- nf-core/tower-action master composite
- nf-core/tower-action master composite
- mshick/add-pr-comment v1 composite
- actions/checkout v2 composite
- actions/checkout v2 composite
- actions/checkout v1 composite
- actions/setup-node v1 composite
- actions/setup-python v1 composite
- actions/upload-artifact v2 composite
- mshick/add-pr-comment v1 composite
- dawidd6/action-download-artifact v2 composite
- marocchino/sticky-pull-request-comment v2 composite
- actions/stale v7 composite
- actions/checkout v3 composite
- actions/setup-node v3 composite