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nf-encyclopedia

A NextFlow pipeline for chromatogram library DIA proteomics workflows

https://github.com/talusbio/nf-encyclopedia

Science Score: 31.0%

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    Found 1 DOI reference(s) in README
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Keywords

bioinformatics data-independent-acquisition nextflow pipeline proteomics workflow
Last synced: 6 months ago · JSON representation ·

Repository

A NextFlow pipeline for chromatogram library DIA proteomics workflows

Basic Info
  • Host: GitHub
  • Owner: TalusBio
  • License: apache-2.0
  • Language: Nextflow
  • Default Branch: main
  • Homepage:
  • Size: 18.4 MB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 3
  • Open Issues: 3
  • Releases: 0
Topics
bioinformatics data-independent-acquisition nextflow pipeline proteomics workflow
Created over 4 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License Citation

README.md

nf-encyclopedia

nf-encyclopedia is a NextFlow pipeline specifically designed to analyze DIA proteomics experiment that leverage chromatogram libraries; however it is perfectly suited to analyze DIA proteomics experiments without chromatogram libraries as well. The nf-encyclopedia connects three open-source tools---MSconvert, EncyclopeDIA, and MSstats---to go from mass spectra to quantified peptides and proteins.

See the nf-encyclopedia documentation

Development

Running Tests

We use the pytest Python package to run our tests. It can be installed using conda:

sh conda env create --name nf_encyclopedia --file=environment.yml conda activate nf_encyclopedia conda install pytest

Once installed, tests can be run from the root directory of the workflow. Run them with:

sh docker pull ghcr.io/talusbio/nf-encyclopedia:latest pytest

References

This pipeline uses code and infrastructure developed and maintained by the nf-core initiative, and reused here under the MIT license.

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.

Credits

This pipeline was originally written by @ricomnl and @wfondrie at Talus Bio. Additionally, @cia23 has spent numerous hours reviewing @wfondrie's messy PRs and performing validation experiments.

Owner

  • Name: Talus Bio
  • Login: TalusBio
  • Kind: organization
  • Location: United States of America

Citation (CITATION.md) 

# Cite nf-encyclopedia

## [nf-encyclopedia]()

> TODO: Add preprint

## Pipeline Tools:

### [MSconvert](https://pubmed.ncbi.nlm.nih.gov/23051804/)

> Chambers, M. C., Maclean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T. A., Brusniak, M.-Y., Paulse, C., Creasy, D., … Mallick, P. (2012). A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology, 30(10), 918–920. https://doi.org/10.1038/nbt.2377

### [EncyclopeDIA](https://pubmed.ncbi.nlm.nih.gov/30510204/)

> Searle, B. C., Pino, L. K., Egertson, J. D., Ting, Y. S., Lawrence, R. T., MacLean, B. X., Villen, J., & MacCoss, M. J. (2018). Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07454-w

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

> Choi, M., Chang, C.-Y., 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. https://doi.org/10.1093/bioinformatics/btu305

## Infrastructure:

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. https://doi.org/10.1038/nbt.3820

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276–278. https://doi.org/10.1038/s41587-020-0439-x

GitHub Events

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Dependencies

.github/workflows/docker.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/metadata-action v3 composite
.github/workflows/docs.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/release.yml actions
  • Actions-R-Us/actions-tagger latest composite
  • actions/checkout v2 composite
.github/workflows/test.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v2 composite
  • docker/build-push-action v2 composite
environment.yml conda
  • bioconductor-msstats 4.2.0.*
  • numpy
  • pandas
  • pytest
  • python 3.10.*
  • r-dplyr
  • r-magrittr
  • r-rlang
  • r-stringr
  • r-tidyr
Dockerfile docker
  • mambaorg/micromamba latest build
  • searlelab/encyclopedia $VERSION build