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Spectra

Low level infrastructure to handle MS spectra

https://github.com/rformassspectrometry/spectra

Science Score: 49.0%

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    Found 2 DOI reference(s) in README
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    3 of 12 committers (25.0%) from academic institutions
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    Low similarity (12.3%) to scientific vocabulary

Keywords

bioconductor hacktoberfest mass-spectrometry metabolomics proteomics rstats

Keywords from Contributors

bioconductor-package motif-analysis motif-enrichment-analysis sequence-logo
Last synced: 6 months ago · JSON representation

Repository

Low level infrastructure to handle MS spectra

Basic Info
Statistics
  • Stars: 41
  • Watchers: 9
  • Forks: 28
  • Open Issues: 42
  • Releases: 0
Topics
bioconductor hacktoberfest mass-spectrometry metabolomics proteomics rstats
Created almost 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog

README.md

Low level infrastructure to handle MS spectra

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R-CMD-check-bioc codecov license years in bioc Ranking by downloads build release build devel

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data.

A description of its functionality and design is available in this preprint.

Spectra provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

A (possibly incomplete) list of available backends (along with a link to the R package providing it) is shown below:

  • MsBackendCompDb (package CompoundDb: provides access to spectra data (spectra and peaks variables) from a CompDb database. Has a small memory footprint because all data (except precursor m/z values) are retrieved on-the-fly from the database.

  • MsBackendDataFrame (package: Spectra): alternative to the MsBackendMemory also keeping all data in memory, but supporting S4 objects as spectra variables because the data is stored internally in a DataFrame.

  • MsBackendHdf5Peaks (package: Spectra): on-disk backend similar to MsBackendMzR, but the peaks data is stored in HDF5 files (general spectra variables are kept in memory).

  • MsBackendHmdbXml (package MsbackendHmdb): allows import of MS data from xml files of the Human Metabolome Database (HMDB). Extends the MsBackendDataFrame and keeps thus all data, after import, in memory.

  • MsBackendMassbank (package MsBackendMassbank): allows to import/export data in MassBank text file format. Extends the MsBackendDataFrame and keeps thus all data, after import, in memory.

  • MsBackendMassbankSql (package MsBackendMassbank): allows to directly connect to a MassBank SQL database to retrieve all MS data and variables. Has a minimal memory footprint because all data is retrieved on-the-fly from the SQL database.

  • MsBackendMemory (package: Spectra): default backend which keeps all data in memory. Optimized for fast processing.

  • MsBackendMetaboLights (package MsBackendMetaboLights): retrieves and caches MS data files from MetaboLights.

  • MsBackendMgf (package MsBackendMgf): allows to import/export data in mascot generic format (MGF). Extends the MsBackendDataFrame and keeps thus all data, after import, in memory.

  • MsBackendMsp (package MsbackendMsp): allows to import/export data in NIST MSP format. Extends the MsBackendDataFrame and keeps thus all data, after import, in memory.

  • MsBackendMzR (package: Spectra): by using the mzR package it supports import of MS data from mzML, mzXML and CDF files. This backend keeps only general spectra variables in memory and retrieves the peaks data (m/z and intensity values) on-the-fly from the original data files. The backend has thus a smaller memory footprint compared to in-memory backends.

  • MsBackendOfflineSql (package MsBackendSql): stores all MS data in a SQL database and has thus a minimal memory footprint. Does, in contrast to MsBackendSql, not keep an active SQL database connection and can thus support parallel processing.

  • MsBackendRawFileReader (package MsBackendRawFileReader): implements a backend for reading MS data from Thermo Fisher Scientific's raw data files using the manufacturer's NewRawFileReader .Net libraries. The package generalizes the functionality introduced by the rawrr package.

  • MsBackendSql (package MsBackendSql): stores all MS data in a SQL database and has thus a minimal memory footprint.

  • MsBackendTimsTof (package MsBackendTimsTof: allows import of data from Bruker TimsTOF raw data files (using the opentimsr R package).

  • MsBackendWeizMass (package MsBackendWeizMass: allows to access MS data from WeizMass MS/MS spectral databases.

For more information see the package homepage.

Installation

The package can be installed with

r install.packages("BiocManager") BiocManager::install("Spectra")

Contributions

Contributions are highly welcome and should follow the contribution guidelines. Also, please check the coding style guidelines in the RforMassSpectrometry vignette and importantly, follow our code of conduct.

Owner

  • Name: RforMassSpectrometry
  • Login: rformassspectrometry
  • Kind: organization
  • Email: maintainer@rformassspectrometry.org

R packages for mass spectrometry

GitHub Events

Total
  • Issues event: 16
  • Watch event: 4
  • Issue comment event: 58
  • Push event: 78
  • Pull request review event: 33
  • Pull request review comment event: 33
  • Pull request event: 30
  • Fork event: 4
  • Create event: 1
Last Year
  • Issues event: 16
  • Watch event: 4
  • Issue comment event: 58
  • Push event: 78
  • Pull request review event: 33
  • Pull request review comment event: 33
  • Pull request event: 30
  • Fork event: 4
  • Create event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 979
  • Total Committers: 12
  • Avg Commits per committer: 81.583
  • Development Distribution Score (DDS): 0.206
Past Year
  • Commits: 73
  • Committers: 6
  • Avg Commits per committer: 12.167
  • Development Distribution Score (DDS): 0.411
Top Committers
Name Email Commits
jorainer j****r@g****m 777
Laurent Gatto l****o@u****e 89
Sebastian Gibb m****l@s****e 32
Philippine Louail p****l@o****m 30
Guitou1 p****f@g****m 16
J Wokaty j****y@s****u 10
Nitesh Turaga n****a@g****m 8
Mar Garcia Aloy m****y@g****m 5
nshahaf n****f@w****l 5
Christian Panse c****e 4
A Wokaty a****y@s****u 2
Jan Stanstrup s****p@g****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2 weizmann.ac.il: 1 sebastiangibb.de: 1 uclouvain.be: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 85
  • Total pull requests: 87
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 20
  • Total pull request authors: 9
  • Average comments per issue: 3.51
  • Average comments per pull request: 1.77
  • Merged pull requests: 73
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 13
  • Pull requests: 34
  • Average time to close issues: 7 days
  • Average time to close pull requests: 6 days
  • Issue authors: 9
  • Pull request authors: 4
  • Average comments per issue: 1.77
  • Average comments per pull request: 1.06
  • Merged pull requests: 27
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jorainer (49)
  • lgatto (10)
  • sgibb (5)
  • cbroeckl (3)
  • cpanse (2)
  • v-v1150n (2)
  • ismaRP (1)
  • sardnar (1)
  • philouail (1)
  • Adafede (1)
  • ricoderks (1)
  • YasinEl (1)
  • schymane (1)
  • michaelwitting (1)
  • felipe-mansoldo (1)
Pull Request Authors
  • jorainer (63)
  • sgibb (8)
  • philouail (5)
  • lgatto (5)
  • guideflandre (2)
  • Ahlammentag (1)
  • stanstrup (1)
  • sneumann (1)
  • mar-garcia (1)
Top Labels
Issue Labels
enhancement (4) question (3) bug (2) backends (2) help wanted (1) good first issue (1) API (1) documentation (1)
Pull Request Labels
documentation (1)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 98,572 total
  • Total dependent packages: 15
  • Total dependent repositories: 0
  • Total versions: 9
  • Total maintainers: 1
bioconductor.org: Spectra

Spectra Infrastructure for Mass Spectrometry Data

  • Versions: 9
  • Dependent Packages: 15
  • Dependent Repositories: 0
  • Downloads: 98,572 Total
Rankings
Dependent repos count: 0.0%
Forks count: 2.8%
Dependent packages count: 3.7%
Stargazers count: 5.6%
Average: 8.6%
Downloads: 30.8%
Maintainers (1)
maintainer@rformassspectrometry.org
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • BiocParallel * depends
  • ProtGenerics >= 1.25.1 depends
  • R >= 4.0.0 depends
  • S4Vectors * depends
  • BiocGenerics * imports
  • IRanges * imports
  • MsCoreUtils >= 1.7.5 imports
  • fs * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • stats * imports
  • tools * imports
  • utils * imports
  • BiocStyle >= 2.5.19 suggests
  • knitr >= 1.1.0 suggests
  • msdata >= 0.19.3 suggests
  • mzR >= 2.19.6 suggests
  • rhdf5 >= 2.32.0 suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat * suggests
  • vdiffr >= 1.0.0 suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite