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quantms-readthedocs

This repository contains the documentation of quantms workflow

https://github.com/bigbio/quantms-readthedocs

Science Score: 44.0%

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    Low similarity (9.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

This repository contains the documentation of quantms workflow

Basic Info
  • Host: GitHub
  • Owner: bigbio
  • License: mit
  • Language: Batchfile
  • Default Branch: main
  • Homepage: https://docs.quantms.org/
  • Size: 27.2 MB
Statistics
  • Stars: 0
  • Watchers: 4
  • Forks: 0
  • Open Issues: 1
  • Releases: 3
Created 10 months ago · Last pushed 6 months ago
Metadata Files
Readme License Code of conduct Citation

README.md

nf-core/quantms nf-core/quantms

Source repository for the Sphinx documentation of the bigbio/quantms Nextflow pipeline.

Docs Creation

The documentation is built by ReadTheDocs. You can see previews of your changes for a PR-specific build on ReadTheDocs project builds, and under the Actions tab of this PR.

Local Build

In order to build the docs, you need to

  1. Install sphinx and additional support packages
  2. Build the package reference files
  3. Run sphinx to create a local html version

Install the docs dependencies of the package (as specified in requirements.txt):

```bash

in main folder

pip install -r requirements.txt ```

Run the following command inside the docs folder to build the HTML:

```bash

build page in docs folder

python setupdocs.py # downloads files from bigbio/quantms/docs folder, # called in conf.py if built on Read The Docs. sphinx-build -n -W --keep-going -b html ./ ./build/ ```

Owner

  • Name: BigBio Stack
  • Login: bigbio
  • Kind: organization
  • Email: proteomicsstack@gmail.com
  • Location: Cambridge, UK

Provide big data solutions Bioinformatics

Citation (CITATIONS.md) 

# nf-core/quantms: 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

- [thermorawfileparser](https://pubmed.ncbi.nlm.nih.gov/31755270/)

  > Hulstaert N, Shofstahl J, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y. ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion. J Proteome Res. 2020 Jan 3;19(1):537-542. doi: 10.1021/acs.jproteome.9b00328. Epub 2019 Dec 6. PMID: 31755270; PMCID: PMC7116465.

- [sdrf-pipelines](https://pubmed.ncbi.nlm.nih.gov/34615866/)

  > Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun. 2021 Oct 6;12(1):5854. doi: 10.1038/s41467-021-26111-3. PMID: 34615866; PMCID: PMC8494749.

- [OpenMS](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Röst HL., Sachsenberg T., Aiche S., Bielow C., Weisser H., Aicheler F., Andreotti S., Ehrlich HC., Gutenbrunner P., Kenar E., Liang X., Nahnsen S., Nilse L., Pfeuffer J., Rosenberger G., Rurik M., Schmitt U., Veit J., Walzer M., Wojnar D., Wolski WE., Schilling O., Choudhary JS, Malmström L., Aebersold R., Reinert K., Kohlbacher O. (2016). OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature methods, 13(9), 741–748. doi: 10.1038/nmeth.3959. PubMed PMID: 27575624; PubMed Central PMCID: PMC5617107.

- [DIA-NN](https://pubmed.ncbi.nlm.nih.gov/31768060/)

  > Demichev V, Messner CB, Vernardis SI, Lilley KS, Ralser M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods. 2020 Jan;17(1):41-44. doi: 10.1038/s41592-019-0638-x. Epub 2019 Nov 25. PMID: 31768060; PMCID: PMC6949130.

- [MSstats](https://www.ncbi.nlm.nih.gov/pubmed/24794931/)

  > Choi M., Chang CY., Clough T., Broudy D., Killeen T., MacLean B., Vitek O. (2014). MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics (Oxford, England), 30(17), 2524–2526. doi: 10.1093/bioinformatics/btu305. PubMed PMID: 24794931.

- [Comet](https://www.ncbi.nlm.nih.gov/pubmed/23148064/)

  > Eng JK., Jahan TA., Hoopmann MR. (2013). Comet: an open-source MS/MS sequence database search tool. Proteomics, 13(1), 22–24. doi: 10.1002/pmic.201200439. PubMed PMID: 23148064

- [MS-GF+](https://www.ncbi.nlm.nih.gov/pubmed/25358478/)

  > Kim S., Pevzner PA. (2014). MS-GF+ makes progress towards a universal database search tool for proteomics. Nature communications, 5, 5277. doi: 10.1038/ncomms6277. PubMed PMID: 25358478; PubMed Central PMCID: PMC5036525

- [Epifany](https://pubmed.ncbi.nlm.nih.gov/31975601/)

  > Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O. EPIFANY: A Method for Efficient High-Confidence Protein Inference. J Proteome Res. 2020 Mar 6;19(3):1060-1072. doi: 10.1021/acs.jproteome.9b00566. Epub 2020 Feb 13. PMID: 31975601; PMCID: PMC7583457.

- [Triqler](https://pubmed.ncbi.nlm.nih.gov/30482846/)

  > The M, Käll L. Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics. Mol Cell Proteomics. 2019 Mar;18(3):561-570. doi: 10.1074/mcp.RA118.001018. Epub 2018 Nov 27. PMID: 30482846; PMCID: PMC6398204.

- [luciphor](https://pubmed.ncbi.nlm.nih.gov/23918812/)
  > Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics. 2013 Nov;12(11):3409-19. doi: 10.1074/mcp.M113.028928. Epub 2013 Aug 5. PMID: 23918812; PMCID: PMC3820951.

## 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)

- [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

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Last Year
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 18
  • Member event: 1
  • Push event: 38
  • Pull request review comment event: 25
  • Pull request review event: 25
  • Pull request event: 11
  • Create event: 7

Dependencies

requirements.txt pypi
  • furo *
  • sphinx *