Package: scpdata 1.13.0

Christophe Vanderaa

scpdata: Single-Cell Proteomics Data Package

The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts.

Authors:Christophe Vanderaa [aut, cre], Laurent Gatto [aut], Enes Ayar [dtc], Samuel Grégoire [dtc]

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scpdata.pdf |scpdata.html✨
scpdata/json (API)
NEWS

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

Peer review:

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

On CRAN:

28 exports 4 stars 1.51 score 117 dependencies 16 scripts

Last updated 5 months agofrom:a2c8b038c1. Checks:OK: 3 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-winNOTEAug 31 2024
R-4.5-linuxNOTEAug 31 2024
R-4.4-winOKAug 31 2024
R-4.4-macOKAug 31 2024

Exports:brunner2022cong2020ACderks2022dou2019_boostingdou2019_lysatesdou2019_mousegregoire2023_mixCTRLguise2024khan2023leduc2022leduc2022_plexDIAleduc2022_pSCoPEliang2020_helapetrosius2023_AstralAMLpetrosius2023_mESschoof2021scpdataspecht2019v2specht2019v3williams2020_lfqwilliams2020_tmtwoo2022_lungwoo2022_macrophagezhu2018MCPzhu2018NC_helazhu2018NC_isletszhu2018NC_lysateszhu2019EL

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbslibcachemcliclueclustercolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrevaluateExperimentHubfansifarverfastmapfilelockfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigplogrplotlyplyrpngpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownRSQLiteS4ArraysS4VectorssassscalesSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc

Contribution guidelines

Christophe Vanderaa, Laurent Gatto

Rendered fromcontribution_guidelines.Rmdusingknitr::rmarkdownon Aug 31 2024.

Last update: 2024-03-11
Started: 2024-02-15

Single Cell Proteomics data sets

Laurent Gatto, Christophe Vanderaa

Rendered fromscpdata.Rmdusingknitr::rmarkdownon Aug 31 2024.

Last update: 2024-02-15
Started: 2019-10-15

Readme and manuals

Help Manual

Help pageTopics
Brunner et al. 2022 (Mol. Syst. Biol.): cell cycle state studybrunner2022
Cong et al. 2020 (Ana. Chem.): HeLa single cellscong2020AC
Derks et al. 2022 - plexDIA (Nat. Biotechnol.): PDAC vs melanoma cells vs monocytesderks2022
Dou et al. 2019 (Anal. Chem.): testing boosting ratiosdou2019_boosting
Dou et al. 2019 (Anal. Chem.): HeLa lysatesdou2019_lysates
Dou et al. 2019 (Anal. Chem.): murine cell linesdou2019_mouse
Grégoire et al. 2023 - mixCTRL (arXiv): benchmark using monocytes/macrophagesgregoire2023_mixCTRL
Guise et al. 2020 (Cell Rep.): postmortem ALS spinal moto neuronsguise2024
Khan et al, 2023 (biorRxiv): Epithelial–Mesenchymal Transitionkhan2023
Deprecated leduc2022 datasetleduc2022
Leduc et al. 2022 - plexDIA (biorRxiv): melanoma cellsleduc2022_plexDIA
Leduc et al. 2022 - pSCoPE (biorRxiv): melanoma cells vs monocytesleduc2022_pSCoPE
Liang et al. 2020 (Anal. Chem.): HeLa cells (MaxQuant preprocessing)liang2020_hela
Petrosius et al. 2023 (bioRxiv): AML hierarchy on Astral.petrosius2023_AstralAML
Petrosius et al, 2023 (Nat. Comm.): Mouse embryonic stem cell (mESC) in different culture conditionspetrosius2023_mES
Schoof et al. 2021 (Nat. Comm.): acute myeloid leukemia differentiationschoof2021
Single-Cell Proteomics Data Packagescpdata-package scpdata
Specht et al. 2019 - SCoPE2 (biorRxiv): macrophages vs monocytes (version 2)specht2019v2
Specht et al. 2019 - SCoPE2 (biorRxiv): macrophages vs monocytes (version 3)specht2019v3
Williams et al. 2020 (Anal. Chem.): MCF10A cell linewilliams2020_lfq
Williams et al. 2020 (Anal. Chem.): 3 AML cell linewilliams2020_tmt
Woo et al. 2022 (Cell Syst.): 26 primary human lung cellswoo2022_lung
Woo et al. 2022 (Cell Syst.): LPS-treated macrophageswoo2022_macrophage
Zhu et al. 2018 (Mol. Cel. Prot.): rat brain laser dissectionszhu2018MCP
Zhu et al. 2018 (Nat. Comm.): HeLa titrationzhu2018NC_hela
Zhu et al. 2018 (Nat. Comm.): human pancreatic isletszhu2018NC_islets
Zhu et al. 2018 (Nat. Comm.): HeLa lysateszhu2018NC_lysates
Zhu et al. 2019 (eLife): chicken utricle cellszhu2019EL