Package: scp 1.21.1

Christophe Vanderaa

scp: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

Authors:Christophe Vanderaa [aut, cre], Laurent Gatto [aut], Léopold Guyot [ctb]

scp_1.21.1.tar.gz
scp_1.21.1.zip(r-4.7)scp_1.21.1.zip(r-4.6)scp_1.21.1.zip(r-4.5)
scp_1.21.1.tgz(r-4.6-any)scp_1.21.1.tgz(r-4.5-any)
scp_1.21.1.tar.gz(r-4.7-any)scp_1.21.1.tar.gz(r-4.6-any)
scp_1.21.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scp/json (API)
NEWS

# Install 'scp' in R:
install.packages('scp', repos = c('https://uclouvain-cbio.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/uclouvain-cbio/scp/issues

Pkgdown/docs site:https://uclouvain-cbio.github.io

Datasets:

On BioConductor:scp-1.23.0(bioc 3.24)scp-1.22.0(bioc 3.23)

geneexpressionproteomicssinglecellmassspectrometrypreprocessingcellbasedassaysbioconductormass-spectrometrysingle-cellsoftware

8.89 score 32 stars 272 scripts 38 exports 100 dependencies

Last updated from:5a3e230dfb. Checks:2 WARNING, 2 OK, 5 ERROR. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING923
source / vignettesOK531
linux-release-x86_64WARNING829
macos-release-arm64ERROR972
macos-oldrel-arm64ERROR698
windows-develERROR462
windows-releaseERROR464
windows-oldrelERROR409
wasm-releaseOK206

Exports:addReducedDimsaggregateFeaturesOverAssayscomputeSCRcumulativeSensitivityCurvedivideByReferencejaccardIndexmedianCVperCellnormalizeSCPpep2qvaluepredictSensitivityreadSCPreadSCPfromDIANNreadSingleCellExperimentreportMissingValuesscpAnnotateResultsscpComponentAggregatescpComponentAnalysisscpComponentBiplotscpComponentPlotscpDifferentialAggregatescpDifferentialAnalysisscpKeepEffectscpModelComponentMethodsscpModelEffectsscpModelFilterNPRatioscpModelFilterPlotscpModelFilterThresholdscpModelFilterThreshold<-scpModelFormulascpModelInputscpModelNamesscpModelResidualsscpModelWorkflowscpRemoveBatchEffectscpVarianceAggregatescpVarianceAnalysisscpVariancePlotscpVolcanoPlot

Dependencies:abindAnnotationFilteraskpassbase64encBiobaseBiocBaseUtilsBiocGenericsbslibcachemcliclueclustercpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfdrtoolfontawesomefsgenericsGenomicRangesggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttrigraphIHWIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelpsymphonymagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmimeMsCoreUtilsMultiAssayExperimentnipalsopensslotelpillarpkgconfigplotlyplyrpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoSingleCellExperimentslamSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

Advanced usage of scp

Laurent Gatto, Christophe Vanderaa

Rendered fromadvanced.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2024-04-08
Started: 2021-07-27

Load Single-Cell Proteomics data using readSCP

Laurent Gatto, Christophe Vanderaa

Rendered fromread_scp.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2025-07-02
Started: 2021-06-21

QFeatures in a nutshell

Laurent Gatto, Christophe Vanderaa

Rendered fromQFeatures_nutshell.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2025-05-28
Started: 2021-07-16

Reporting missing values for Single Cell Proteomics

Christophe Vanderaa, Laurent Gatto

Rendered fromreporting_missing_values.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2024-04-08
Started: 2023-05-22

Single Cell Proteomics data modelling using scplainer

Laurent Gatto, Christophe Vanderaa

Rendered fromscp_data_modelling.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2025-07-02
Started: 2024-04-02

Single Cell Proteomics data processing and analysis

Laurent Gatto, Christophe Vanderaa

Rendered fromscp.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2025-07-02
Started: 2020-08-18

Readme and manuals

Help Manual

Help pageTopics
Add scplainer Component Analysis ResultsaddReducedDims
Aggregate features over multiple assaysaggregateFeaturesOverAssays aggregateFeaturesOverAssays-deprecated
Compute the sample over carrier ratio (SCR)computeSCR
Cumulative sensitivity curvecumulativeSensitivityCurve predictSensitivity
Divide assay columns by a reference columndivideByReference
Compute the pairwise Jaccard indexjaccardIndex
Minimally processed single-cell proteomics data setleduc_minimal
Compute the median coefficient of variation (CV) per cellmedianCVperCell
Example MaxQuant/SCoPE2 outputmqScpData
Normalize single-cell proteomics (SCP) datanormalizeSCP
Compute q-valuespep2qvalue
Read single-cell proteomics tabular datareadSCP readSCPfromDIANN readSingleCellExperiment
Four metrics to report missing valuesreportMissingValues
Single cell sample annotationsampleAnnotation
Single Cell QFeatures datascp1
Annotate single-cell proteomics analysis outputscpAnnotateResults
scplainer: linear models to understand mass spectrometry-based single-cell proteomics datascplainer
Class to store the results of single-cell proteomics modellingclass:ScpModel ScpModel ScpModel-class scpModelEffects scpModelFilterNPRatio scpModelFilterThreshold scpModelFilterThreshold<- scpModelFormula scpModelInput scpModelNames scpModelResiduals
Correct single-cell proteomics datascpKeepEffect ScpModel-DataCorrection scpRemoveBatchEffect
Differential abundance analysis for single-cell proteomicsscpDifferentialAggregate scpDifferentialAnalysis ScpModel-DifferentialAnalysis scpVolcanoPlot
Analysis of variance for single-cell proteomicsScpModel-VarianceAnalysis scpVarianceAggregate scpVarianceAnalysis scpVariancePlot
Modelling single-cell proteomics dataScpModel-Workflow scpModelFilterPlot scpModelWorkflow
Component analysis for single cell proteomicsscpComponentAggregate scpComponentAnalysis scpComponentBiplot scpComponentPlot ScpModel-ComponentAnalysis scpModelComponentMethods
Class to store the components of an estimated model for a featureclass:ScpModelFit ScpModelFit ScpModelFit-class