Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Single cell proteomics data processing
Basic Info
- Host: GitHub
- Owner: UCLouvain-CBIO
- Language: R
- Default Branch: master
- Homepage: https://uclouvain-cbio.github.io/scp/index.html
- Size: 70.1 MB
Statistics
- Stars: 29
- Watchers: 2
- Forks: 3
- Open Issues: 22
- Releases: 0
Topics
Metadata Files
README.md
Single cell proteomics data processing
The scp package is used to process and analyse mass
spectrometry-based single cell proteomics data. It relies on the
QFeatures
package to manage and process
SingleCellExperiment
or SummarizedExperiment
objects.
Installation
To install the stable version from Bioconductor:
r
if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install("scp")
To install the devel version from GitHub, you first need to
ensure that you are using the devel release of Bioconductor and make
sure your installed libraries are valid.
r
BiocManager::install(version = "devel")
stopifnot(BiocManager::valid())
Then, you can install scp from Github.
r
BiocManager::install("UCLouvain-CBIO/scp")
Citation
To cite the scp package in publications use:
Vanderaa, Christophe, and Laurent Gatto. 2023. “Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics.” Journal of Proteome Research 22 (9): 2775–84.
Vanderaa Christophe and Laurent Gatto. The current state of single-cell proteomics data analysis. Current Protocols 3 (1): e658.; doi: https://doi.org/10.1002/cpz1.658 (2023).
Vanderaa Christophe and Laurent Gatto. Replication of Single-Cell Proteomics Data Reveals Important Computational Challenges. Expert Review of Proteomics, 1–9 (2021).
Asking for help
Feel free to use Github
issues or the
Bioconductor support site to ask
question or report problems with scp.
License
The scp code is provided under a permissive
Artistic 2.0 license.
The documentation, including the manual pages and the vignettes, are
distributed under a
CC BY-SA license.
Contributions
Contributions are welcome, and should ideally be provdied through a Github pull request. Feel free to discuss any more non-trivial suggestions or changes first in an issue.
Contributors
Owner
- Name: Computational Biology and Bioinformatics at UCLouvain
- Login: UCLouvain-CBIO
- Kind: organization
- Location: Brussels, Belgium
- Website: https://lgatto.github.io/cbio-lab/
- Repositories: 9
- Profile: https://github.com/UCLouvain-CBIO
GitHub Events
Total
- Issues event: 12
- Watch event: 4
- Issue comment event: 47
- Push event: 33
- Pull request review comment event: 11
- Pull request review event: 14
- Pull request event: 14
- Fork event: 2
- Create event: 2
Last Year
- Issues event: 12
- Watch event: 4
- Issue comment event: 47
- Push event: 33
- Pull request review comment event: 11
- Pull request review event: 14
- Pull request event: 14
- Fork event: 2
- Create event: 2
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 8
- Total pull requests: 6
- Average time to close issues: 3 months
- Average time to close pull requests: 4 days
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 1.25
- Average comments per pull request: 1.67
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 8
- Pull requests: 6
- Average time to close issues: 3 months
- Average time to close pull requests: 4 days
- Issue authors: 4
- Pull request authors: 3
- Average comments per issue: 1.25
- Average comments per pull request: 1.67
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- edemmott (5)
- cvanderaa (3)
- lgatto (3)
- leopoldguyot (2)
- samgregoire (2)
- shimin-chen (2)
- prvst (1)
- Axe2Ash (1)
- michabirklbauer (1)
Pull Request Authors
- cvanderaa (8)
- leopoldguyot (8)
- lgatto (3)
- michabirklbauer (1)
- edemmott (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 13,065 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: scp
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
- Homepage: https://UCLouvain-CBIO.github.io/scp
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/scp/inst/doc/scp.pdf
- License: Artistic-2.0
-
Latest release: 1.18.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- QFeatures >= 1.3.5 depends
- R >= 4.0 depends
- MsCoreUtils * imports
- MultiAssayExperiment * imports
- S4Vectors * imports
- SingleCellExperiment * imports
- SummarizedExperiment * imports
- dplyr * imports
- magrittr * imports
- matrixStats * imports
- methods * imports
- rlang * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- ggplot2 * suggests
- impute * suggests
- knitr * suggests
- patchwork * suggests
- preprocessCore * suggests
- rmarkdown * suggests
- scater * suggests
- sva * suggests
- testthat * suggests
- uwot * suggests
- vsn * suggests
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite