xcms
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
Science Score: 59.0%
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○CITATION.cff file
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✓DOI references
Found 1 DOI reference(s) in README -
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11 of 60 committers (18.3%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (15.2%) to scientific vocabulary
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Repository
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
Basic Info
- Host: GitHub
- Owner: sneumann
- License: other
- Language: R
- Default Branch: devel
- Size: 142 MB
Statistics
- Stars: 201
- Watchers: 21
- Forks: 82
- Open Issues: 207
- Releases: 0
Topics
Metadata Files
README.md
Welcome to the home of xcms!
The xcms R package provides functionality to efficiently preprocess LC-MS (as well as GC-MS and LC-MS/MS) data. Please see the package documentation for more information and examples and news for the latest changes. An example preprocessing workflow is shown in the main package vignette. See also the excellent [Metabonaut] resource for a more detailed and complete end-to-end data analysis workflow for LC-MS data.
Installation
xcms is part of Bioconductor and relies and integrates with various Bioconductor packages. The preferred way to install xcms is using the BiocManager package, that will install the latest stable version of xcms and ensures all required packages from the same Bioconductor release are installed and available as well:
r
install.packages()
Version 4
Version 4 adds native support for the
Spectra package to xcms and
allows to perform the pre-processing on MsExperiment objects (from the
MsExperiment. The new
supported data containers (Spectra, MsExperiment and XcmsExperiment) allow
more flexible analyses and seamless future extensions to additional types of
data (such as ion mobility data). Ultimately, these changes will also allow
easier integration of xcms with other R packages such as
MsFeatures or
MetaboAnnotation.
While it is suggested that users switch to the newer data and result objects, all functionality from version 3 and before remain fully supported.
Version 3
Version >= 3 of the xcms package are updated and partially re-written versions
of the original xcms package. The version number 3 was selected to avoid
confusions with the xcms2 (http://pubs.acs.org/doi/abs/10.1021/ac800795f)
software. While providing all of the original software's functionality, xcms
version >= 3 aims at:
1) Better integration into the Bioconductor framework:
- Make use and extend classes defined in the MSnbase package.
- Implement class versioning (Biobase's Versioned class).
- Use BiocParallel for parallel processing.
2) Implementation of validation methods for all classes to ensure data
integrity.
3) Easier and faster access to raw spectra data.
4) Cleanup of the source code:
- Remove obsolete and redundant functionality (getEIC, rawEIC etc).
- Unify interfaces, i.e. implement a layer of base functions accessing all
analysis methods (which are implemented in C, C++ or R).
5) Using a more consistent naming scheme of methods that follows established
naming conventions (e.g. correspondence instead of grouping).
6) Update, improve and extend the documentation.
7) Establishing a layer of base R-functions that interface all analysis
methods. These should take M/Z, retention time (or scan index) and intensity
values as input along with optional arguments for the downstream functions
(implemented in C, C++ or R). The input arguments should be basic R objects
(numeric vectors) thus enabling easy integration of analysis methods in other
R packages.
8) The user interface's analysis methods should take the (raw) data object and a
parameter class, that is used for dispatching to the corresponding analysis
algorithm.
9) Add unit tests.
Discussions and suggestions are welcome: https://github.com/sneumann/xcms/issues
Contribution
Contributions to the xcms package are more than welcome, whether under the form of ideas, documentation, code, packages, ... For a contribution guideline please see the guideline for the RforMassSpectrometry initiative. For a seamless integration, contributors are expected to adhere to the RforMassSpectrometry coding syle.
Code of Conduct
As contributors and maintainers of the package, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities. See the RforMassSpectrometry Code of Conduct for more information.
Owner
- Name: Steffen Neumann
- Login: sneumann
- Kind: user
- Repositories: 29
- Profile: https://github.com/sneumann
GitHub Events
Total
- Issues event: 29
- Watch event: 19
- Delete event: 1
- Issue comment event: 96
- Push event: 56
- Pull request review comment event: 62
- Pull request review event: 58
- Pull request event: 13
- Fork event: 1
- Create event: 9
Last Year
- Issues event: 29
- Watch event: 19
- Delete event: 1
- Issue comment event: 96
- Push event: 56
- Pull request review comment event: 62
- Pull request review event: 58
- Pull request event: 13
- Fork event: 1
- Create event: 9
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| jorainer | j****r@g****m | 947 |
| Steffen Neumann | s****n@i****e | 767 |
| Ralf Tautenhahn | r****h@i****e | 392 |
| s.neumann | s****n@b****8 | 380 |
| r.tautenhahn | r****n@b****8 | 196 |
| Paul Benton | h****n@s****u | 164 |
| Colin Smith | c****n@c****g | 130 |
| p.benton | p****n@b****8 | 82 |
| Philippine Louail | p****l@o****m | 73 |
| Dan Tenenbaum | d****a@f****g | 68 |
| colin | c****n@b****8 | 65 |
| Michael Lawrence | l****i@i****u | 56 |
| wkumler | w****r@u****u | 49 |
| d.tenenbaum | d****m@b****8 | 34 |
| Patrick Aboyoun | u****n | 32 |
| m.lawrence | m****e@b****8 | 28 |
| Herve Pages | h****s@f****g | 28 |
| p.aboyoun | p****n@b****8 | 16 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 16 |
| pablovgd | 7****d | 16 |
| Conley Christopher | c****r@g****m | 16 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 10 |
| Seth Falcon | s****n@f****g | 10 |
| Bioconductor Git-SVN Bridge | b****c@b****g | 9 |
| c.conley | c****y@b****8 | 9 |
| Jan Stanstrup | s****p@g****m | 9 |
| Hendrik Treutler | h****e@i****e | 8 |
| Johannes Rainer | jo@m****u | 7 |
| Michael Witting | m****g@h****e | 6 |
| and 30 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 115
- Total pull requests: 57
- Average time to close issues: 4 months
- Average time to close pull requests: 2 months
- Total issue authors: 68
- Total pull request authors: 11
- Average comments per issue: 4.43
- Average comments per pull request: 2.46
- Merged pull requests: 46
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 25
- Pull requests: 17
- Average time to close issues: 16 days
- Average time to close pull requests: 18 days
- Issue authors: 19
- Pull request authors: 4
- Average comments per issue: 3.28
- Average comments per pull request: 1.06
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jorainer (10)
- sneumann (9)
- Pembs (5)
- CLUES-Emory (4)
- pablovgd (4)
- jmorim (3)
- stanstrup (3)
- v-v1150n (3)
- Pascallio (2)
- chuyaowang (2)
- JasonBason (2)
- crestre (2)
- jzhou19 (2)
- plyush1993 (2)
- felipe-mansoldo (2)
Pull Request Authors
- jorainer (47)
- philouail (14)
- pablovgd (5)
- sneumann (5)
- NorStorz (2)
- RogerGinBer (1)
- genefisher (1)
- hechth (1)
- hpbenton (1)
- dmurdoch (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 913,303 total
- Total dependent packages: 15
- Total dependent repositories: 0
- Total versions: 11
- Total maintainers: 1
bioconductor.org: xcms
LC-MS and GC-MS Data Analysis
- Homepage: https://github.com/sneumann/xcms
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.pdf
- License: GPL (>= 2) + file LICENSE
-
Latest release: 4.6.3
published 8 months ago
Rankings
Maintainers (1)
Dependencies
- 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
- BiocParallel >= 1.8.0 depends
- MSnbase >= 2.21.4 depends
- R >= 4.0.0 depends
- Rgraphviz * enhances
- XML * enhances
- rgl * enhances
- Biobase * imports
- BiocGenerics * imports
- IRanges * imports
- MassSpecWavelet >= 1.61.3 imports
- MsCoreUtils * imports
- MsFeatures * imports
- ProtGenerics >= 1.25.1 imports
- RANN * imports
- RColorBrewer * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- lattice * imports
- methods * imports
- mzR >= 2.25.3 imports
- plyr * imports
- robustbase * imports
- BiocStyle * suggests
- MALDIquant * suggests
- MsBackendMgf * suggests
- Spectra >= 1.1.17 suggests
- caTools * suggests
- faahKO * suggests
- knitr >= 1.1.0 suggests
- magrittr * suggests
- msdata >= 0.25.1 suggests
- multtest * suggests
- ncdf4 * suggests
- pander * suggests
- pheatmap * suggests
- progress * suggests
- rmarkdown * suggests
- signal * suggests
- testthat * suggests