Package: scpdata 1.13.1

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'))

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

On CRAN:

experimentdata expressiondata experimenthub reproducibleresearch massspectrometrydata proteome singlecelldata packagetypedata

5.58 score 6 stars 16 scripts 31 exports 117 dependencies

Last updated 25 days agofrom:0d3a371b8d. Checks:OK: 1 ERROR: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 28 2024
R-4.5-win	ERROR	Oct 29 2024
R-4.5-linux	ERROR	Oct 29 2024
R-4.4-win	ERROR	Oct 29 2024
R-4.4-mac	ERROR	Oct 29 2024

Exports:brunner2022 cong2020AC derks2022 dou2019_boosting dou2019_lysates dou2019_mouse gregoire2023_mixCTRL guise2024 hu2023_K562 hu2023_oocyte khan2023 krull2024 leduc2022 leduc2022_plexDIA leduc2022_pSCoPE liang2020_hela petrosius2023_AstralAML petrosius2023_mES schoof2021 scpdata specht2019v2 specht2019v3 williams2020_lfq williams2020_tmt woo2022_lung woo2022_macrophage zhu2018MCP zhu2018NC_hela zhu2018NC_islets zhu2018NC_lysates zhu2019EL

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass base64enc Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob bslib cachem cli clue cluster colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest dplyr evaluate ExperimentHub fansi farver fastmap filelock fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime MsCoreUtils MultiAssayExperiment munsell nlme openssl pillar pkgconfig plogr plotly plyr png promises ProtGenerics purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

Contribution guidelines

Christophe Vanderaa, Laurent Gatto

Rendered fromcontribution_guidelines.Rmdusingknitr::rmarkdownon Oct 28 2024.

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

Single Cell Proteomics data sets

Laurent Gatto, Christophe Vanderaa

Rendered fromscpdata.Rmdusingknitr::rmarkdownon Oct 28 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Brunner et al. 2022 (Mol. Syst. Biol.): cell cycle state study	brunner2022
Cong et al. 2020 (Ana. Chem.): HeLa single cells	cong2020AC
Derks et al. 2022 - plexDIA (Nat. Biotechnol.): PDAC vs melanoma cells vs monocytes	derks2022
Dou et al. 2019 (Anal. Chem.): testing boosting ratios	dou2019_boosting
Dou et al. 2019 (Anal. Chem.): HeLa lysates	dou2019_lysates
Dou et al. 2019 (Anal. Chem.): murine cell lines	dou2019_mouse
Grégoire et al. 2023 - mixCTRL (arXiv): benchmark using monocytes/macrophages	gregoire2023_mixCTRL
Guise et al. 2020 (Cell Rep.): postmortem ALS spinal moto neurons	guise2024
Khan et al, 2023 (biorRxiv): Epithelial–Mesenchymal Transition	khan2023
Deprecated leduc2022 dataset	leduc2022
Leduc et al. 2022 - plexDIA (biorRxiv): melanoma cells	leduc2022_plexDIA
Leduc et al. 2022 - pSCoPE (biorRxiv): melanoma cells vs monocytes	leduc2022_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 conditions	petrosius2023_mES
Schoof et al. 2021 (Nat. Comm.): acute myeloid leukemia differentiation	schoof2021
Single-Cell Proteomics Data Package	scpdata-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 line	williams2020_lfq
Williams et al. 2020 (Anal. Chem.): 3 AML cell line	williams2020_tmt
Woo et al. 2022 (Cell Syst.): 26 primary human lung cells	woo2022_lung
Woo et al. 2022 (Cell Syst.): LPS-treated macrophages	woo2022_macrophage
Zhu et al. 2018 (Mol. Cel. Prot.): rat brain laser dissections	zhu2018MCP
Zhu et al. 2018 (Nat. Comm.): HeLa titration	zhu2018NC_hela
Zhu et al. 2018 (Nat. Comm.): human pancreatic islets	zhu2018NC_islets
Zhu et al. 2018 (Nat. Comm.): HeLa lysates	zhu2018NC_lysates
Zhu et al. 2019 (eLife): chicken utricle cells	zhu2019EL