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Open Source Science

SWATH2stats

https://github.com/peterblattmann/swath2stats

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 11 committers (18.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics bioconductor bioc proteomics regionreport core-package gc-ms feature-detection
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 3
  • Releases: 0
Created almost 9 years ago · Last pushed over 2 years ago

https://github.com/peterblattmann/SWATH2stats/blob/master/ 



# SWATH2stats

This package is intended to transform extracted SWATH/DIA data from the
OpenSWATH or other (e.g.Spectronaut) software into a format
directly-usable by statistics packages (e.g.mapDIA, PECA, MSstats)
while performing filtering, annotation and FDR assessment if necessary.

## Analyzing SWATH/DIA data

How to extract SWATH/DIA data before using SWATH2stats with OpenSWATH
can be found here: 

## Usage

SWATH2stats is a Bioconductor package. Go to

to see all information related to installation. Importantly there exists
both a release and development version.

## Contribution

Please feel free to comment and post issues or pull requests on github.

## Publication

For the publication describing this package, see:


## References

  - Blattmann P, Heusel M, Aebersold R. SWATH2stats: An R/Bioconductor
    Package to Process and Convert Quantitative SWATH-MS Proteomics Data
    for Downstream Analysis Tools. PLoS ONE 11(4): e0153160 (2016). doi:
    10.1371/journal.pone.0153160.

  - Rost HL, Rosenberger G, Navarro P, Gillet L, Miladinovic SM,
    Schubert OT, Wolski W, Collins BC, Malmstrom J, Malmstrom L,
    Aebersold R. OpenSWATH enables automated, targeted analysis of
    data-independent acquisition MS data. Nature Biotechnology. 2014
    Mar;32(3):219-23. doi: 10.1038/nbt.2841.

  - Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O.
    MSstats: an R package for statistical analysis of quantitative mass
    spectrometry-based proteomic experiments.Bioinformatics. 2014 Sep
    1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305.

  - Rosenberger G, Ludwig C, Rost HL, Aebersold R, Malmstrom L. aLFQ: an
    R-package for estimating absolute protein quantities from label-free
    LC-MS/MS proteomics data. Bioinformatics. 2014 Sep 1;30(17):2511-3.
    doi: 10.1093/bioinformatics/btu200.

  - Suomi T., Corthals G., Nevalainen O.S., and Elo L.L. (2015). Using
    Peptide-Level Proteomics Data for Detecting Differentially Expressed
    Proteins. J Proteome Res. Nov 6;14(11):4564-70. doi:
    10.1021/acs.jproteome.5b00363.

  - Suomi, T. and Elo L.L. (2017). Enhanced differential expression
    statistics for data-independent acquisition proteomics" Scientific
    Reports 7, Article number: 5869.doi:10.1038/s41598-017-05949-y

Owner

  • Name: Peter
  • Login: peterblattmann
  • Kind: user

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 176
  • Total Committers: 11
  • Avg Commits per committer: 16.0
  • Development Distribution Score (DDS): 0.557
Past Year
  • Commits: 6
  • Committers: 3
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.667
Top Committers
Name Email Commits
Peter Blattmann b****n@i****h 78
Peter Blattmann p****n@b****h 59
Nitesh Turaga n****a@g****m 14
Herve Pages h****s@f****g 8
Dan Tenenbaum d****a@f****g 6
J Wokaty j****y@s****u 2
Hervé Pagès h****s@f****g 2
vobencha v****a@g****m 2
J Wokaty j****y 2
vobencha v****n@r****g 2
James Hester j****r@f****g 1
Committer Domains (Top 20 + Academic)
fredhutch.org: 2 fhcrc.org: 2 roswellpark.org: 1 sph.cuny.edu: 1 bluewin.ch: 1 imsb.biol.ethz.ch: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 4
  • Total pull requests: 2
  • Average time to close issues: over 2 years
  • Average time to close pull requests: over 1 year
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.25
  • Average comments per pull request: 6.5
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • abelew (1)
  • awd97 (1)
  • Matthias313 (1)
  • dpanyard (1)
Pull Request Authors
  • abelew (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 18,973 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: SWATH2stats

Transform and Filter SWATH Data for Statistical Packages

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 18,973 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 18.4%
Average: 18.7%
Stargazers count: 29.0%
Downloads: 45.9%
Maintainers (1)
peter_blattmann@bluewin.ch
Last synced: 11 months ago

Dependencies

.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
DESCRIPTION cran
  • R >= 2.10.0 depends
  • MSstats * enhances
  • PECA * enhances
  • aLFQ * enhances
  • biomaRt * imports
  • data.table * imports
  • ggplot2 * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • reshape2 * imports
  • stats * imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests