DaparToolshedData 0.99.21
Mass-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.
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.
library("DaparToolshedData")
DaparToolshedData()## 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 NATo install the package:
if (!require("BiocManager"))
install.packages("BiocManager")
BiocManager::install("DaparToolshedData")Load datasets with (example for the Exp1_R25_prot dataset)
GetData('Exp1_R25_prot')## see ?DaparToolshedData and browseVignettes('DaparToolshedData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## An instance of class QFeatures (type: bulk) with 1 set:
##
## [1] Convert: SummarizedExperiment with 2384 rows and 6 columnssessionInfo()## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] DaparToolshedData_0.99.21 BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 dplyr_1.2.1
## [3] blob_1.3.0 filelock_1.0.3
## [5] Biostrings_2.81.9 fastmap_1.2.0
## [7] lazyeval_0.2.3 BiocFileCache_3.3.0
## [9] digest_0.6.39 lifecycle_1.0.5
## [11] cluster_2.1.8.3 ProtGenerics_1.45.0
## [13] KEGGREST_1.53.6 RSQLite_3.53.3
## [15] magrittr_2.0.5 compiler_4.6.1
## [17] rlang_1.3.0 sass_0.4.10
## [19] tools_4.6.1 igraph_2.3.3
## [21] yaml_2.3.12 knitr_1.52
## [23] S4Arrays_1.13.0 bit_4.6.0
## [25] curl_8.0.0 DelayedArray_0.39.6
## [27] plyr_1.8.9 abind_1.4-8
## [29] withr_3.0.3 purrr_1.2.2
## [31] BiocGenerics_0.59.12 grid_4.6.1
## [33] stats4_4.6.1 ExperimentHub_3.3.2
## [35] MASS_7.3-66 MultiAssayExperiment_1.39.1
## [37] SummarizedExperiment_1.43.0 cli_3.6.6
## [39] rmarkdown_2.32 crayon_1.5.3
## [41] generics_0.1.4 otel_0.2.0
## [43] httr_1.4.9 reshape2_1.4.5
## [45] BiocBaseUtils_1.15.1 DBI_1.3.0
## [47] cachem_1.1.0 stringr_1.6.0
## [49] AnnotationDbi_1.75.2 AnnotationFilter_1.37.0
## [51] BiocManager_1.30.27 XVector_0.53.0
## [53] matrixStats_1.5.0 vctrs_0.7.3
## [55] Matrix_1.7-6 jsonlite_2.0.0
## [57] bookdown_0.48 IRanges_2.47.5
## [59] S4Vectors_0.51.9 bit64_4.8.6
## [61] clue_0.3-68 tidyr_1.3.2
## [63] jquerylib_0.1.4 glue_1.8.1
## [65] QFeatures_1.23.2 stringi_1.8.9
## [67] BiocVersion_3.24.0 GenomicRanges_1.65.4
## [69] tibble_3.3.1 pillar_1.11.1
## [71] rappdirs_0.3.4 htmltools_0.5.9
## [73] Seqinfo_1.3.2 R6_2.6.1
## [75] dbplyr_2.6.0 httr2_1.3.0
## [77] evaluate_1.0.5 lattice_0.23-1
## [79] Biobase_2.73.2 AnnotationHub_4.3.2
## [81] png_0.1-9 memoise_2.0.1
## [83] bslib_0.12.0 Rcpp_1.1.2
## [85] SparseArray_1.13.2 xfun_0.60
## [87] MsCoreUtils_1.25.4 MatrixGenerics_1.25.0
## [89] pkgconfig_2.0.3