inst/scripts/make-metadata.R
In UCLouvain-CBIO/scpdata: Single-Cell Proteomics Data Package
####---- EXPERIMENTHUB METADATA TABLE ----####
meta <- list(
data.frame(
Title = "specht2019v2",
Description = paste0("SCP expression data for monocytes (U-937) and macrophages ",
"at PSM, peptide and protein level"),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "CSV",
SourceUrl = "https://drive.google.com/drive/folders/1Zhjik_JFjCQNIVjg63-fooJ4K0HZxWjV",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "GoogleDrive",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/specht2019v2.Rda",
PublicationDate = as.Date("2019/12/5"),
NumberAssays = 179,
PreprocessingSoftware = "MaxQuant,DART-ID",
LabelingProtocol = "TMT-11,TMT-16",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "specht2019v3",
Description = paste0("SCP expression data for more monocytes (U-937) and ",
"macrophages at PSM, peptide and protein level"),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "CSV",
SourceUrl = "https://drive.google.com/drive/folders/1Zhjik_JFjCQNIVjg63-fooJ4K0HZxWjV",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "GoogleDrive",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/specht2019v3.Rda",
PublicationDate = as.Date("2020/10/04"),
NumberAssays = 179,
PreprocessingSoftware = "MaxQuant,DART-ID",
LabelingProtocol = "TMT-11,TMT-16",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "dou2019_lysates",
Description = paste0("SCP expression data for Hela digests (0.2 or 10 ng) at ",
"PSM and protein level"),
BiocVersion = "3.14",
Genome = NA_character_,
SourceType = "XLS/XLSX",
SourceUrl = "ftp://massive.ucsd.edu/MSV000084110/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/dou2019_lysates.Rda",
PublicationDate = as.Date("2019/10/15"),
NumberAssays = 4,
PreprocessingSoftware = "MS-GF+,MASIC",
LabelingProtocol = "TMT-10",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "dou2019_mouse",
Description = paste0("SCP expression data for C10, SVEC or Raw cells at ",
"PSM and protein level"),
BiocVersion = "3.14",
Genome = NA_character_,
SourceType = "XLS/XLSX",
SourceUrl = "ftp://massive.ucsd.edu/MSV000084110/",
SourceVersion = NA_character_,
Species = "Mus musculus",
TaxonomyId = 10090,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/dou2019_mouse.Rda",
PublicationDate = as.Date("2019/10/15"),
NumberAssays = 14,
PreprocessingSoftware = "MS-GF+,MASIC",
LabelingProtocol = "TMT-10",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "dou2019_boosting",
Description = paste0("SCP expression data for C10, SVEC or Raw cells ",
"and 3 boosters (0, 5 or 50 ng) at PSM and protein level"),
BiocVersion = "3.14",
Genome = NA_character_,
SourceType = "XLS/XLSX",
SourceUrl = "ftp://massive.ucsd.edu/MSV000084110/",
SourceVersion = NA_character_,
Species = "Mus musculus",
TaxonomyId = 10090,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/dou2019_boosting.Rda",
PublicationDate = as.Date("2019/10/15"),
NumberAssays = 8,
PreprocessingSoftware = "MS-GF+,MASIC",
LabelingProtocol = "TMT-10",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "zhu2018MCP",
Description = paste0("Near SCP expression data for micro-dissected rat ",
"brain samples (50, 100, or 200 um width) at PSM level"),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/07/PXD008844",
SourceVersion = NA_character_,
Species = "Rattus norvegicus",
TaxonomyId = 10116,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2018MCP.Rda",
PublicationDate = as.Date("2018/09/01"),
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
NumberAssays = 4,
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "zhu2018NC_hela",
Description = paste0("Near SCP expression data for HeLa samples (aproximately ",
"12, 40, or 140 cells) at PSM level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006847",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2018NC_hela.Rda",
PublicationDate = as.Date("2018/02/28"),
NumberAssays = 4,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "zhu2018NC_lysates",
Description = paste0("Near SCP expression data for HeLa lysates (10, 40 and ",
"140 cell equivalent) at PSM level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006847",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2018NC_lysates.Rda",
PublicationDate = as.Date("2018/02/28"),
NumberAssays = 4,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "zhu2018NC_islets",
Description = paste0("Near SCP expression data for micro-dissected human ",
"pancreas samples (control patients or type 1 ",
"diabetes) at PSM level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006847",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2018NC_islets.Rda",
PublicationDate = as.Date("2018/02/28"),
NumberAssays = 4,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "cong2020AC",
Description = paste0("SCP expression data for Hela cells at PSM, peptide ",
"and protein level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/02/PXD016921",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/cong2020AC.Rda",
PublicationDate = as.Date("2020/01/02"),
NumberAssays = 9,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "zhu2019EL",
Description = paste0("SCP expression data for chicken utricle samples (1, ",
"3, 5 or 20 cells) at PSM, peptide and protein level"),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD014256",
SourceVersion = NA_character_,
Species = "Gallus gallus",
TaxonomyId = 9031,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2019EL.Rda",
PublicationDate = as.Date("2019/11/04"),
NumberAssays = 63,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "liang2020_hela",
Description = paste0("Expression data for HeLa cells (0, 1, ",
"10, 150, 500 cells) at PSM, peptide and ",
"protein level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD021882/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/liang2020_hela.Rda",
PublicationDate = as.Date("2020/12/22"),
NumberAssays = 17,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "schoof2021",
Description = paste0("Single-cell proteomics data from ",
"OCI-AML8227 cell culture to reconstruct ",
"the cellular hierarchy."),
BiocVersion = "3.14",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "http://ftp.pride.ebi.ac.uk/pride/data/archive/2021/05/PXD020586/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/schoof2021.Rda",
PublicationDate = as.Date("2021/06/07"),
NumberAssays = 194,
PreprocessingSoftware = "ProteomeDiscoverer",
LabelingProtocol = "TMT-16",
PsmsAvailable = TRUE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "williams2020_lfq",
Description = paste0("Single-cell label free proteomics data ",
"from a MCF10A cell line culture."),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000085230/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/williams2020_lfq.Rda",
PublicationDate = as.Date("2020/08/04"),
NumberAssays = 9,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "williams2020_tmt",
Description = paste0("Single-cell proteomics data ",
"from three acute myeloid leukemia cell ",
"line culture (MOLM-14, K562, CMK)."),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000085230/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/williams2020_tmt.Rda",
PublicationDate = as.Date("2020/08/04"),
NumberAssays = 4,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "TMT-11",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "derks2022",
Description = paste0("Single-cell and bulk (100-cell) ",
"proteomics data of PDAC, melanoma cells ",
"and monocytes."),
BiocVersion = "3.16",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089093/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/derks2022.Rda",
PublicationDate = as.Date("2022/07/14"),
NumberAssays = 66,
PreprocessingSoftware = "DIA-NN",
LabelingProtocol = "mTRAQ",
PsmsAvailable = TRUE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "brunner2022",
Description = paste0("Single-cell proteomics data of cell ",
"cycle stages in HeLa."),
BiocVersion = "3.16",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://www.ebi.ac.uk/pride/archive/projects/PXD024043",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/brunner2022.Rda",
PublicationDate = as.Date("2022/02/08"),
NumberAssays = 435,
PreprocessingSoftware = "DIA-NN",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "leduc2022_pSCoPE",
Description = paste0("Single-cell proteomics data ",
"of 878 melanoma cells and 877 ",
"monocytes (pSCoPE)."),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089159/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/leduc2022_pSCoPE.Rda",
PublicationDate = as.Date("2022/03/30"),
NumberAssays = 138,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "TMT-18",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "leduc2022_plexDIA",
Description = paste0("Single-cell proteomics data ",
"of 126 melanoma cells (plexDIA)."),
BiocVersion = "3.18",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089159/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/leduc2022_plexDIA.Rda",
PublicationDate = as.Date("2022/12/06"),
NumberAssays = 48,
PreprocessingSoftware = "DIA-NN",
LabelingProtocol = "mTRAQ-3",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "woo2022_macrophage",
Description = paste0("Single-cell proteomics data ",
"from LPS-treated macrophages."),
BiocVersion = "3.18",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000085937/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/woo2022_macrophage.Rda",
PublicationDate = as.Date("2022/05/18"),
NumberAssays = 5,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "woo2022_lung",
Description = paste0("Single-cell proteomics data ",
"from primary human lung cells."),
BiocVersion = "3.18",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000085937/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/woo2022_lung.Rda",
PublicationDate = as.Date("2022/05/18"),
NumberAssays = 5,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "gregoire2023_mixCTRL",
Description = paste0("Single-cell proteomics data ",
"from two monocyte cell lines"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://www.ebi.ac.uk/pride/archive/projects/PXD046211",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Samuel Gregoire <samuel.gregoire@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/gregoire2023_mixCTRL.Rda",
PublicationDate = as.Date("2024/01/22"),
NumberAssays = 119,
PreprocessingSoftware = "Sage",
LabelingProtocol = "TMT-16",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "khan2023",
Description = paste0("Single-cell proteomics data ",
"of 421 MCF-10A cells undergoing ",
"EMT triggered by TGFβ"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://drive.google.com/drive/folders/1zCsRKWNQuAz5msxx0DfjDrIe6pUjqQmj",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/khan2023.Rda",
PublicationDate = as.Date("2023/12/21"),
NumberAssays = 47,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "TMTPro 16plex",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "guise2024",
Description = paste0("Single-cell proteomics data ",
"of 108 postmortem CTL or ALS spinal ",
"moto neurons"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/v05/MSV000092119/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/guise2024.rda",
PublicationDate = as.Date("2024/01/05"),
NumberAssays = 47,
PreprocessingSoftware = "Proteome Discoverer",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "petrosius2023_mES",
Description = paste0("Mouse embryonic stem cells across ground-state (m2i) ",
"and differentiation-permissive (m15) culture conditions."),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://dataverse.uclouvain.be/dataset.xhtml?persistentId=doi:10.14428/DVN/EMAVLT",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "Dataverse",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/petrosius2023_mES.Rda",
PublicationDate = as.Date("2024/04/09"),
NumberAssays = 605,
PreprocessingSoftware = "Spectronaut",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "petrosius2023_AstralAML",
Description = paste0("Single-cell proteomics data ",
"of 4 cell types from the OCI-AML8227 ",
"model."),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://dataverse.uclouvain.be/dataset.xhtml?persistentId=doi:10.14428/DVN/4DSPJM",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "Dataverse",
Maintainer = "Samuel Gregoire <samuel.gregoire@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/petrosius2023_AstralAML.Rda",
PublicationDate = as.Date("2023/06/08"),
NumberAssays = 217,
PreprocessingSoftware = "Spectronaut",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "krull2024",
Description = paste0("Single-cell proteomics data ",
"IFN-γ response of U-2 OS cells"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://www.ebi.ac.uk/pride/archive/projects/PXD053464",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/krull2024.Rda",
PublicationDate = as.Date("2024/10/24"),
NumberAssays = 159,
PreprocessingSoftware = "DIA-NN",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "hu2023_K562",
Description = paste0("Single-cell proteomics data of K562 cells"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089625/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "SingleCellExperiment",
DispatchClass = "Rda",
RDataPath = "scpdata/hu2023_K562.Rda",
PublicationDate = as.Date("2024/10/24"),
NumberAssays = 1,
PreprocessingSoftware = "Proteome Discoverer",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "hu2023_oocyte",
Description = paste0("Single-cell proteomics data of oocytes"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089625/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "SingleCellExperiment",
DispatchClass = "Rda",
RDataPath = "scpdata/hu2023_oocyte.Rda",
PublicationDate = as.Date("2024/10/24"),
NumberAssays = 1,
PreprocessingSoftware = "Proteome Discoverer",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
)
)
metadata <- do.call(rbind, meta)
write.csv(metadata,
file = here::here("inst", "extdata", "metadata.csv"),
row.names = FALSE)
stopifnot(file.exists(pkg_source <- here()))
AnnotationHubData::makeAnnotationHubMetadata(pathToPackage = pkg_source,
fileName = "metadata.csv")
UCLouvain-CBIO/scpdata documentation built on Oct. 29, 2024, 4:22 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
####---- EXPERIMENTHUB METADATA TABLE ----####
meta <- list(
data.frame(
Title = "specht2019v2",
Description = paste0("SCP expression data for monocytes (U-937) and macrophages ",
"at PSM, peptide and protein level"),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "CSV",
SourceUrl = "https://drive.google.com/drive/folders/1Zhjik_JFjCQNIVjg63-fooJ4K0HZxWjV",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "GoogleDrive",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/specht2019v2.Rda",
PublicationDate = as.Date("2019/12/5"),
NumberAssays = 179,
PreprocessingSoftware = "MaxQuant,DART-ID",
LabelingProtocol = "TMT-11,TMT-16",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "specht2019v3",
Description = paste0("SCP expression data for more monocytes (U-937) and ",
"macrophages at PSM, peptide and protein level"),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "CSV",
SourceUrl = "https://drive.google.com/drive/folders/1Zhjik_JFjCQNIVjg63-fooJ4K0HZxWjV",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "GoogleDrive",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/specht2019v3.Rda",
PublicationDate = as.Date("2020/10/04"),
NumberAssays = 179,
PreprocessingSoftware = "MaxQuant,DART-ID",
LabelingProtocol = "TMT-11,TMT-16",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "dou2019_lysates",
Description = paste0("SCP expression data for Hela digests (0.2 or 10 ng) at ",
"PSM and protein level"),
BiocVersion = "3.14",
Genome = NA_character_,
SourceType = "XLS/XLSX",
SourceUrl = "ftp://massive.ucsd.edu/MSV000084110/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/dou2019_lysates.Rda",
PublicationDate = as.Date("2019/10/15"),
NumberAssays = 4,
PreprocessingSoftware = "MS-GF+,MASIC",
LabelingProtocol = "TMT-10",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "dou2019_mouse",
Description = paste0("SCP expression data for C10, SVEC or Raw cells at ",
"PSM and protein level"),
BiocVersion = "3.14",
Genome = NA_character_,
SourceType = "XLS/XLSX",
SourceUrl = "ftp://massive.ucsd.edu/MSV000084110/",
SourceVersion = NA_character_,
Species = "Mus musculus",
TaxonomyId = 10090,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/dou2019_mouse.Rda",
PublicationDate = as.Date("2019/10/15"),
NumberAssays = 14,
PreprocessingSoftware = "MS-GF+,MASIC",
LabelingProtocol = "TMT-10",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "dou2019_boosting",
Description = paste0("SCP expression data for C10, SVEC or Raw cells ",
"and 3 boosters (0, 5 or 50 ng) at PSM and protein level"),
BiocVersion = "3.14",
Genome = NA_character_,
SourceType = "XLS/XLSX",
SourceUrl = "ftp://massive.ucsd.edu/MSV000084110/",
SourceVersion = NA_character_,
Species = "Mus musculus",
TaxonomyId = 10090,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/dou2019_boosting.Rda",
PublicationDate = as.Date("2019/10/15"),
NumberAssays = 8,
PreprocessingSoftware = "MS-GF+,MASIC",
LabelingProtocol = "TMT-10",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "zhu2018MCP",
Description = paste0("Near SCP expression data for micro-dissected rat ",
"brain samples (50, 100, or 200 um width) at PSM level"),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/07/PXD008844",
SourceVersion = NA_character_,
Species = "Rattus norvegicus",
TaxonomyId = 10116,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2018MCP.Rda",
PublicationDate = as.Date("2018/09/01"),
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
NumberAssays = 4,
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "zhu2018NC_hela",
Description = paste0("Near SCP expression data for HeLa samples (aproximately ",
"12, 40, or 140 cells) at PSM level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006847",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2018NC_hela.Rda",
PublicationDate = as.Date("2018/02/28"),
NumberAssays = 4,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "zhu2018NC_lysates",
Description = paste0("Near SCP expression data for HeLa lysates (10, 40 and ",
"140 cell equivalent) at PSM level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006847",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2018NC_lysates.Rda",
PublicationDate = as.Date("2018/02/28"),
NumberAssays = 4,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "zhu2018NC_islets",
Description = paste0("Near SCP expression data for micro-dissected human ",
"pancreas samples (control patients or type 1 ",
"diabetes) at PSM level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006847",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2018NC_islets.Rda",
PublicationDate = as.Date("2018/02/28"),
NumberAssays = 4,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = FALSE,
Notes = NA_character_
),
data.frame(
Title = "cong2020AC",
Description = paste0("SCP expression data for Hela cells at PSM, peptide ",
"and protein level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/02/PXD016921",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/cong2020AC.Rda",
PublicationDate = as.Date("2020/01/02"),
NumberAssays = 9,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "zhu2019EL",
Description = paste0("SCP expression data for chicken utricle samples (1, ",
"3, 5 or 20 cells) at PSM, peptide and protein level"),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD014256",
SourceVersion = NA_character_,
Species = "Gallus gallus",
TaxonomyId = 9031,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/zhu2019EL.Rda",
PublicationDate = as.Date("2019/11/04"),
NumberAssays = 63,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "liang2020_hela",
Description = paste0("Expression data for HeLa cells (0, 1, ",
"10, 150, 500 cells) at PSM, peptide and ",
"protein level"),
BiocVersion = "3.13",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD021882/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/liang2020_hela.Rda",
PublicationDate = as.Date("2020/12/22"),
NumberAssays = 17,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "schoof2021",
Description = paste0("Single-cell proteomics data from ",
"OCI-AML8227 cell culture to reconstruct ",
"the cellular hierarchy."),
BiocVersion = "3.14",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "http://ftp.pride.ebi.ac.uk/pride/data/archive/2021/05/PXD020586/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/schoof2021.Rda",
PublicationDate = as.Date("2021/06/07"),
NumberAssays = 194,
PreprocessingSoftware = "ProteomeDiscoverer",
LabelingProtocol = "TMT-16",
PsmsAvailable = TRUE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "williams2020_lfq",
Description = paste0("Single-cell label free proteomics data ",
"from a MCF10A cell line culture."),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000085230/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/williams2020_lfq.Rda",
PublicationDate = as.Date("2020/08/04"),
NumberAssays = 9,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "williams2020_tmt",
Description = paste0("Single-cell proteomics data ",
"from three acute myeloid leukemia cell ",
"line culture (MOLM-14, K562, CMK)."),
BiocVersion = "3.15",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000085230/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/williams2020_tmt.Rda",
PublicationDate = as.Date("2020/08/04"),
NumberAssays = 4,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "TMT-11",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "derks2022",
Description = paste0("Single-cell and bulk (100-cell) ",
"proteomics data of PDAC, melanoma cells ",
"and monocytes."),
BiocVersion = "3.16",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089093/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/derks2022.Rda",
PublicationDate = as.Date("2022/07/14"),
NumberAssays = 66,
PreprocessingSoftware = "DIA-NN",
LabelingProtocol = "mTRAQ",
PsmsAvailable = TRUE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "brunner2022",
Description = paste0("Single-cell proteomics data of cell ",
"cycle stages in HeLa."),
BiocVersion = "3.16",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://www.ebi.ac.uk/pride/archive/projects/PXD024043",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/brunner2022.Rda",
PublicationDate = as.Date("2022/02/08"),
NumberAssays = 435,
PreprocessingSoftware = "DIA-NN",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "leduc2022_pSCoPE",
Description = paste0("Single-cell proteomics data ",
"of 878 melanoma cells and 877 ",
"monocytes (pSCoPE)."),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089159/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/leduc2022_pSCoPE.Rda",
PublicationDate = as.Date("2022/03/30"),
NumberAssays = 138,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "TMT-18",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "leduc2022_plexDIA",
Description = paste0("Single-cell proteomics data ",
"of 126 melanoma cells (plexDIA)."),
BiocVersion = "3.18",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089159/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/leduc2022_plexDIA.Rda",
PublicationDate = as.Date("2022/12/06"),
NumberAssays = 48,
PreprocessingSoftware = "DIA-NN",
LabelingProtocol = "mTRAQ-3",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "woo2022_macrophage",
Description = paste0("Single-cell proteomics data ",
"from LPS-treated macrophages."),
BiocVersion = "3.18",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000085937/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/woo2022_macrophage.Rda",
PublicationDate = as.Date("2022/05/18"),
NumberAssays = 5,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "woo2022_lung",
Description = paste0("Single-cell proteomics data ",
"from primary human lung cells."),
BiocVersion = "3.18",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000085937/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/woo2022_lung.Rda",
PublicationDate = as.Date("2022/05/18"),
NumberAssays = 5,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "gregoire2023_mixCTRL",
Description = paste0("Single-cell proteomics data ",
"from two monocyte cell lines"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://www.ebi.ac.uk/pride/archive/projects/PXD046211",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Samuel Gregoire <samuel.gregoire@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/gregoire2023_mixCTRL.Rda",
PublicationDate = as.Date("2024/01/22"),
NumberAssays = 119,
PreprocessingSoftware = "Sage",
LabelingProtocol = "TMT-16",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "khan2023",
Description = paste0("Single-cell proteomics data ",
"of 421 MCF-10A cells undergoing ",
"EMT triggered by TGFβ"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://drive.google.com/drive/folders/1zCsRKWNQuAz5msxx0DfjDrIe6pUjqQmj",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/khan2023.Rda",
PublicationDate = as.Date("2023/12/21"),
NumberAssays = 47,
PreprocessingSoftware = "MaxQuant",
LabelingProtocol = "TMTPro 16plex",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "guise2024",
Description = paste0("Single-cell proteomics data ",
"of 108 postmortem CTL or ALS spinal ",
"moto neurons"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/v05/MSV000092119/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Christophe Vanderaa <christophe.vanderaa@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/guise2024.rda",
PublicationDate = as.Date("2024/01/05"),
NumberAssays = 47,
PreprocessingSoftware = "Proteome Discoverer",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "petrosius2023_mES",
Description = paste0("Mouse embryonic stem cells across ground-state (m2i) ",
"and differentiation-permissive (m15) culture conditions."),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://dataverse.uclouvain.be/dataset.xhtml?persistentId=doi:10.14428/DVN/EMAVLT",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "Dataverse",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/petrosius2023_mES.Rda",
PublicationDate = as.Date("2024/04/09"),
NumberAssays = 605,
PreprocessingSoftware = "Spectronaut",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "petrosius2023_AstralAML",
Description = paste0("Single-cell proteomics data ",
"of 4 cell types from the OCI-AML8227 ",
"model."),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://dataverse.uclouvain.be/dataset.xhtml?persistentId=doi:10.14428/DVN/4DSPJM",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "Dataverse",
Maintainer = "Samuel Gregoire <samuel.gregoire@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/petrosius2023_AstralAML.Rda",
PublicationDate = as.Date("2023/06/08"),
NumberAssays = 217,
PreprocessingSoftware = "Spectronaut",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = TRUE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "krull2024",
Description = paste0("Single-cell proteomics data ",
"IFN-γ response of U-2 OS cells"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "https://www.ebi.ac.uk/pride/archive/projects/PXD053464",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "PRIDE",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "QFeatures",
DispatchClass = "Rda",
RDataPath = "scpdata/krull2024.Rda",
PublicationDate = as.Date("2024/10/24"),
NumberAssays = 159,
PreprocessingSoftware = "DIA-NN",
LabelingProtocol = "LFQ",
PsmsAvailable = TRUE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "hu2023_K562",
Description = paste0("Single-cell proteomics data of K562 cells"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089625/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "SingleCellExperiment",
DispatchClass = "Rda",
RDataPath = "scpdata/hu2023_K562.Rda",
PublicationDate = as.Date("2024/10/24"),
NumberAssays = 1,
PreprocessingSoftware = "Proteome Discoverer",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
),
data.frame(
Title = "hu2023_oocyte",
Description = paste0("Single-cell proteomics data of oocytes"),
BiocVersion = "3.19",
Genome = NA_character_,
SourceType = "TXT",
SourceUrl = "ftp://massive.ucsd.edu/MSV000089625/",
SourceVersion = NA_character_,
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "MassIVE",
Maintainer = "Enes Sefa Ayar <enes.ayar@uclouvain.be>",
RDataClass = "SingleCellExperiment",
DispatchClass = "Rda",
RDataPath = "scpdata/hu2023_oocyte.Rda",
PublicationDate = as.Date("2024/10/24"),
NumberAssays = 1,
PreprocessingSoftware = "Proteome Discoverer",
LabelingProtocol = "LFQ",
PsmsAvailable = FALSE,
PeptidesAvailable = FALSE,
ProteinsAvailable = TRUE,
ContainsSingleCells = TRUE,
Notes = NA_character_
)
)
metadata <- do.call(rbind, meta)
write.csv(metadata,
file = here::here("inst", "extdata", "metadata.csv"),
row.names = FALSE)
stopifnot(file.exists(pkg_source <- here()))
AnnotationHubData::makeAnnotationHubMetadata(pathToPackage = pkg_source,
fileName = "metadata.csv")
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