DaparToolshed data using Bioconductor's ExperimentHub
9 June 2026
Source:vignettes/DaparToolshedData.Rmd
DaparToolshedData.RmdMass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32.
Introduction
The DaparToolshedData package provides example
quantitative data from proteomics experiments. The data are served
through the ExperimentHub infrastructure, which allows
download them only ones and cache them for further use. Currently
available data are summarised in the table below and details in the next
section.
## Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
## 'DelayedArray::makeNindexFromArrayViewport' when loading 'SummarizedExperiment'## Title
## 1 Exp1_R25_prot
## 2 Exp1_R25_pept
## 3 Exp1_R2_prot
## 4 Exp1_R2_pept
## 5 Exp2_R2_prot
## 6 Exp2_R2_pept
## 7 Exp2_R10_prot
## 8 Exp2_R10_pept
## 9 Exp2_R100_prot
## 10 Exp2_R100_pept
## Description
## 1 Exp1_R25_prot 2 conditions, 3 replicates each and 2384 proteins, represented as a MultiAssayExperiment.
## 2 Exp1_R25_pept 2 conditions, 3 replicates each and 13919 peptides, represented as a MultiAssayExperiment.
## 3 Exp1_R2_prot 2 conditions, 3 replicates each and 2394 proteins, represented as a MultiAssayExperiment.
## 4 Exp2_R2_pept 2 conditions, 3 replicates each and 14048 peptides, represented as a MultiAssayExperiment.
## 5 Exp2_R2_prot 2 conditions, 3 replicates each and 948 proteins, represented as a MultiAssayExperiment.
## 6 Exp2_R2_pept 2 conditions, 3 replicates each and 5390 peptides, represented as a MultiAssayExperiment.
## 7 Exp2_R10_prot 2 conditions, 3 replicates each and 948 proteins, represented as a MultiAssayExperiment.
## 8 Exp2_R100_pept 2 conditions, 3 replicates each and 5684 peptides, represented as a MultiAssayExperiment.
## 9 Exp2_R100_prot 2 conditions, 3 replicates each and 923 proteins, represented as a MultiAssayExperiment.
## 10 Exp2_R100_pept 2 conditions, 3 replicates each and 5684 peptides, represented as a MultiAssayExperiment.
## BiocVersion Genome SourceType SourceUrl
## 1 3.23 NA RData https://zenodo.org/records/18592150
## 2 3.23 NA RData https://zenodo.org/records/18592150
## 3 3.23 NA RData https://zenodo.org/records/18592150
## 4 3.23 NA RData https://zenodo.org/records/18592150
## 5 3.23 NA RData https://zenodo.org/records/18592150
## 6 3.23 NA RData https://zenodo.org/records/18592150
## 7 3.23 NA RData https://zenodo.org/records/18592150
## 8 3.23 NA RData https://zenodo.org/records/18592150
## 9 3.23 NA RData https://zenodo.org/records/18592150
## 10 3.23 NA RData https://zenodo.org/records/18592150
## SourceVersion Species TaxonomyId Coordinate_1_based DataProvider
## 1 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 2 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 3 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 4 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 5 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 6 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 7 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 8 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 9 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## 10 Feb 10 2026 Homo sapiens NA TRUE EDyP-lab
## Maintainer RDataClass
## 1 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 2 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 3 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 4 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 5 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 6 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 7 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 8 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 9 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## 10 Samuel Wieczorek <samuel.wieczorek@cea.fr> MultiAssayExperiment
## DispatchClass Location_Prefix
## 1 FilePath https://zenodo.org/
## 2 FilePath https://zenodo.org/
## 3 FilePath https://zenodo.org/
## 4 FilePath https://zenodo.org/
## 5 FilePath https://zenodo.org/
## 6 FilePath https://zenodo.org/
## 7 FilePath https://zenodo.org/
## 8 FilePath https://zenodo.org/
## 9 FilePath https://zenodo.org/
## 10 FilePath https://zenodo.org/
## RDataPath Tags Notes
## 1 records/18592150/files/Exp1_R25_prot.RData NA NA
## 2 records/18592150/files/Exp1_R25_pept.RData NA NA
## 3 records/18592150/files/Exp1_R2_prot.RData NA NA
## 4 records/18592150/files/Exp1_R2_pept.RData NA NA
## 5 records/18592150/files/Exp2_R2_prot.RData NA NA
## 6 records/18592150/files/Exp2_R2_pept.RData NA NA
## 7 records/18592150/files/Exp2_R10_prot.RData NA NA
## 8 records/18592150/files/Exp2_R10_pept.RData NA NA
## 9 records/18592150/files/Exp2_R100_prot.RData NA NA
## 10 records/18592150/files/Exp2_R100_pept.RData NA NAInstallation
To install the package:
if (!require("BiocManager"))
install.packages("BiocManager")
BiocManager::install("DaparToolshedData")sessionInfo()
## R version 4.6.0 (2026-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] DaparToolshedData_0.99.17 BiocStyle_2.40.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 dplyr_1.2.1
## [3] blob_1.3.0 Biostrings_2.80.1
## [5] filelock_1.0.3 fastmap_1.2.0
## [7] lazyeval_0.2.3 BiocFileCache_3.2.0
## [9] digest_0.6.39 lifecycle_1.0.5
## [11] cluster_2.1.8.2 ProtGenerics_1.44.0
## [13] KEGGREST_1.52.0 RSQLite_3.53.1
## [15] magrittr_2.0.5 compiler_4.6.0
## [17] rlang_1.2.0 sass_0.4.10
## [19] tools_4.6.0 igraph_2.3.2
## [21] yaml_2.3.12 knitr_1.51
## [23] S4Arrays_1.12.0 htmlwidgets_1.6.4
## [25] bit_4.6.0 curl_7.1.0
## [27] DelayedArray_0.38.2 plyr_1.8.9
## [29] abind_1.4-8 purrr_1.2.2
## [31] BiocGenerics_0.58.1 desc_1.4.3
## [33] grid_4.6.0 stats4_4.6.0
## [35] ExperimentHub_3.2.0 MASS_7.3-65
## [37] MultiAssayExperiment_1.38.0 SummarizedExperiment_1.42.0
## [39] cli_3.6.6 crayon_1.5.3
## [41] rmarkdown_2.31 ragg_1.5.2
## [43] generics_0.1.4 otel_0.2.0
## [45] httr_1.4.8 reshape2_1.4.5
## [47] DBI_1.3.0 cachem_1.1.0
## [49] stringr_1.6.0 AnnotationDbi_1.74.0
## [51] AnnotationFilter_1.36.0 BiocManager_1.30.27
## [53] XVector_0.52.0 matrixStats_1.5.0
## [55] vctrs_0.7.3 Matrix_1.7-5
## [57] jsonlite_2.0.0 bookdown_0.46
## [59] IRanges_2.46.0 S4Vectors_0.50.1
## [61] bit64_4.8.2 clue_0.3-68
## [63] systemfonts_1.3.2 tidyr_1.3.2
## [65] jquerylib_0.1.4 glue_1.8.1
## [67] pkgdown_2.2.0 QFeatures_1.22.0
## [69] stringi_1.8.7 BiocVersion_3.23.1
## [71] GenomicRanges_1.64.0 tibble_3.3.1
## [73] pillar_1.11.1 rappdirs_0.3.4
## [75] htmltools_0.5.9 Seqinfo_1.2.0
## [77] R6_2.6.1 dbplyr_2.5.2
## [79] httr2_1.2.2 textshaping_1.0.5
## [81] evaluate_1.0.5 lattice_0.22-9
## [83] Biobase_2.72.0 AnnotationHub_4.2.0
## [85] png_0.1-9 memoise_2.0.1
## [87] bslib_0.11.0 Rcpp_1.1.1-1.1
## [89] SparseArray_1.12.2 xfun_0.58
## [91] MsCoreUtils_1.24.0 fs_2.1.0
## [93] MatrixGenerics_1.24.0 pkgconfig_2.0.3