Data

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Open Source Science

https://github.com/bioconductor-source/scp

https://github.com/bioconductor-source/scp

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • Language: R
  • Default Branch: devel
  • Size: 50.8 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog

README.md

Project Status: Active – The project has reached a stable, usable state and is being actively developed. codecov.io R-CMD-check-bioc Bioconductor-devel Build Status license

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 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.

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

GitHub Events

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Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
DESCRIPTION cran
  • QFeatures >= 1.13.5 depends
  • R >= 4.3.0 depends
  • IHW * imports
  • MsCoreUtils * imports
  • MultiAssayExperiment * imports
  • RColorBrewer * imports
  • S4Vectors * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • ggplot2 * imports
  • ggrepel * imports
  • matrixStats * imports
  • metapod * imports
  • methods * imports
  • nipals * imports
  • stats * imports
  • utils * imports
  • BiocGenerics * suggests
  • BiocStyle * suggests
  • MsDataHub >= 1.3.3 suggests
  • impute * suggests
  • knitr * suggests
  • patchwork * suggests
  • preprocessCore * suggests
  • rmarkdown * suggests
  • scater * suggests
  • scpdata * suggests
  • sva * suggests
  • testthat * suggests
  • uwot * suggests
  • vdiffr * suggests
  • vsn * suggests