Package: MsDataHub 1.3.4

Laurent Gatto

MsDataHub: Mass Spectrometry Data on ExperimentHub

The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

Authors:Laurent Gatto [aut, cre], Kristina Gomoryova [ctb], Johannes Rainer [aut]

MsDataHub_1.3.4.tar.gz
MsDataHub_1.3.4.zip(r-4.5)MsDataHub_1.3.4.zip(r-4.4)
MsDataHub_1.3.4.tgz(r-4.4-any)
MsDataHub_1.3.4.tar.gz(r-4.5-noble)MsDataHub_1.3.4.tar.gz(r-4.4-noble)
MsDataHub_1.3.4.tgz(r-4.4-emscripten)MsDataHub_1.3.4.tgz(r-4.3-emscripten)
MsDataHub.pdf |MsDataHub.html✨
MsDataHub/json (API)
NEWS

# Install 'MsDataHub' in R:

install.packages('MsDataHub', repos = c('https://rformassspectrometry.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rformassspectrometry/msdatahub/issues

On BioConductor:MsDataHub-1.5.0(bioc 3.20)MsDataHub-1.4.0(bioc 3.19)

experimenthubsoftware massspectrometry proteomics metabolomics bioconductor data mass-spectrometry

4.65 score 1 stars 2 scripts 13 exports 60 dependencies

Last updated 8 months agofrom:b3d4ef741f. Checks:OK: 5. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 30 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 30 2024
R-4.4-mac	OK	Oct 30 2024

Exports:benchmarkingDIA.tsv cptac_a_b_c_peptides.txt cptac_a_b_peptides.txt cptac_peptides.txt ko15.CDF MsDataHub PestMix1_DDA.mzML PestMix1_SWATH.mzML Report.Derks2022.plexDIA.tsv TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz X20171016_POOL_POS_1_105.134.mzML X20171016_POOL_POS_3_105.134.mzML

Dependencies:AnnotationDbi AnnotationHub askpass Biobase BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr dplyr ExperimentHub fansi fastmap filelock generics GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pillar pkgconfig plogr png purrr R6 rappdirs rlang RSQLite S4Vectors stringi stringr sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XVector yaml zlibbioc

Mass Spectrometry Data on ExperimentHub

Laurent Gatto

Rendered fromMsDataHub.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-04-09
Started: 2022-11-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
DIA benchmarking data	benchmarkingDIA benchmarkingDIA.tsv
MS data in CDF format	cdf ko15.CDF
CPTAC label-free data	cptac cptac_a_b_c_peptides.txt cptac_a_b_peptides.txt cptac_peptides.txt
All MsDataHub datasets	MsDataHub
PXD000001 Proteomics Data	PXD000001 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML.gz TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz
Derks 2022 plexDIA data	Report.Derks2022.plexDIA Report.Derks2022.plexDIA.tsv
AB Sciex LC-MS data files	20171016_POOL_POS_1_105-134.mzML 20171016_POOL_POS_3_105-134.mzML sciex X20171016_POOL_POS_1_105.134.mzML X20171016_POOL_POS_3_105.134.mzML
Triple TOF SWATH Data	PestMix1_DDA.mzML PestMix1_SWATH.mzML TripleTOF