Package: artMS 1.31.0

David Jimenez-Morales

artMS: Analytical R tools for Mass Spectrometry

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Authors:David Jimenez-Morales [aut, cre], Alexandre Rosa Campos [aut, ctb], John Von Dollen [aut], Nevan Krogan [aut], Danielle Swaney [aut, ctb]

artMS_1.31.0.tar.gz
artMS_1.31.0.zip(r-4.7)artMS_1.31.0.zip(r-4.6)artMS_1.31.0.zip(r-4.5)
artMS_1.31.0.tgz(r-4.6-any)artMS_1.31.0.tgz(r-4.5-any)
artMS_1.31.0.tar.gz(r-4.7-any)artMS_1.31.0.tar.gz(r-4.6-any)
artMS_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
artMS/json (API)

# Install 'artMS' in R:

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

Bug tracker:https://github.com/biodavidjm/artms/issues

Datasets:

artms_config - ArtMS configuration template
artms_data_corum_mito_database - CORUM Protein Complexes database use for complex enrichment analysis
artms_data_pathogen_LPN - LPN PATHOGEN: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) UNIPROT IDS
artms_data_pathogen_TB - TB PATHOGEN: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) UNIPROTS IDS
artms_data_ph_config - ArtMS configuration for the available PH dataset
artms_data_ph_contrast - Contrast example for the PH dataset
artms_data_ph_evidence - Evidence file example
artms_data_ph_keys - Keys File Example
artms_data_ph_msstats_modelqc - MSstats modelQC example
artms_data_ph_msstats_results - MSstats results example
artms_data_randomDF - Random data set

On BioConductor:artMS-1.31.0(bioc 3.24)artMS-1.29.0(bioc 3.23)

proteomics differentialexpression biomedicalinformatics systemsbiology massspectrometry annotation qualitycontrol genesetenrichment clustering normalization immunooncology multiplecomparison analysis analytical ap-ms bioconductor bioinformatics mass-spectrometry phosphoproteomics post-translational-modification quantitative-analysis

6.61 score 14 stars 21 scripts 2 mentions 33 exports 134 dependencies

Last updated from:4f07b3978e. Checks:8 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	263
linux-devel-x86_64	ERROR	383
source / vignettes	OK	384
linux-release-x86_64	ERROR	408
macos-release-arm64	ERROR	195
macos-oldrel-arm64	ERROR	221
windows-devel	ERROR	268
windows-release	ERROR	335
windows-oldrel	ERROR	366
wasm-release	OK	253

Exports:artmsAnalysisQuantifications artmsAnnotateSpecie artmsAnnotationUniprot artmsAvgIntensityRT artmsChangeColumnName artmsConvertMetabolomics artmsDataPlots artmsEnrichLog2fc artmsEnrichProfiler artmsEvidenceToSaintExpress artmsEvidenceToSAINTq artmsFilterEvidenceContaminants artmsGeneratePhSiteExtended artmsIsEvidenceNewVersion artmsIsSpeciesSupported artmsLeaveOnlyUniprotEntryID artmsMapUniprot2Entrez artmsMergeEvidenceAndKeys artmsMsstatsSummary artmsPhosfateOutput artmsPhotonOutput artmsPlotHeatmapQuant artmsProtein2SiteConversion artmsQualityControlEvidenceBasic artmsQualityControlEvidenceExtended artmsQualityControlMetabolomics artmsQualityControlSummaryExtended artmsQuantification artmsResultsWide artmsSILACtoLong artmsSpectralCounts artmsVolcanoPlot artmsWriteConfigYamlFile

Dependencies:ade4 AnnotationDbi askpass backports base64enc Biobase BiocGenerics Biostrings bit bit64 bitops blob boot bslib cachem caTools checkmate circlize cli cluster colorspace corrplot cpp11 crayon crosstalk curl data.table DBI digest dplyr evaluate farver fastmap fontawesome formatR fs futile.logger futile.options generics getopt ggdendro ggplot2 ggrepel GlobalOptions glue gplots gridExtra gtable gtools highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma lme4 log4r magrittr marray MASS Matrix memoise mime minqa MSstats MSstatsConvert nlme nloptr openssl openxlsx org.Hs.eg.db otel pheatmap pillar pixmap pkgconfig plotly plyr png preprocessCore promises purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown RSQLite S4Vectors S7 sass scales segmented Seqinfo seqinr shape sp statmod stringi stringr survival sys tibble tidyr tidyselect tinytex UpSetR utf8 vctrs VennDiagram viridisLite withr xfun XVector yaml zip

artMS: Analytical R Tools for Mass Spectrometry

Rendered fromartMS_vignette.Rmdusingknitr::rmarkdown

Last update: 2021-07-14
Started: 2018-06-13

Help page	Topics
artMS configuration template	artms_config
CORUM Protein Complexes database use for complex enrichment analysis	artms_data_corum_mito_database
LPN PATHOGEN: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) UNIPROT IDS	artms_data_pathogen_LPN
TB PATHOGEN: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) UNIPROTS IDS	artms_data_pathogen_TB
artMS configuration for the available PH dataset	artms_data_ph_config
Contrast example for the PH dataset	artms_data_ph_contrast
Evidence file example	artms_data_ph_evidence
Keys File Example	artms_data_ph_keys
MSstats modelQC example	artms_data_ph_msstats_modelqc
MSstats results example	artms_data_ph_msstats_results
Random data set	artms_data_randomDF
Analysis of the Relative Quantifications	artmsAnalysisQuantifications
Adding a column with the species name	artmsAnnotateSpecie
Annotate table with Gene Symbol and Name based on Uniprot ID(s)	artmsAnnotationUniprot
Summarize average intensity and retention time per protein	artmsAvgIntensityRT
Change a specific column name in a given data.frame	artmsChangeColumnName
Convert Markview Metabolomics file (alignment table) into a artMS compatible format	artmsConvertMetabolomics
Individual Normalized abundance dot plots for every protein	artmsDataPlots
Enrichment of changes in protein abundance or PTMs	artmsEnrichLog2fc
Enrichment analysis using GprofileR	artmsEnrichProfiler
MaxQuant evidence file to SAINTexpress format	artmsEvidenceToSaintExpress
MaxQuant evidence file to SAINTq format	artmsEvidenceToSAINTq
Remove contaminants and empty proteins from the MaxQuant evidence file	artmsFilterEvidenceContaminants
Generate ph-site specific detailed file	artmsGeneratePhSiteExtended
Check if a given evidencee file was generated by a new version of MaxQuant (v>1)	artmsIsEvidenceNewVersion
Check if a species is supported and available	artmsIsSpeciesSupported
Leave only the Entry ID from a typical full Uniprot IDs in a given column	artmsLeaveOnlyUniprotEntryID
Map GENE SYMBOL, NAME, AND ENTREZID to a vector of Uniprot IDS	artmsMapUniprot2Entrez
Merge evidence.txt (or summary.txt) with keys.txt files	artmsMergeEvidenceAndKeys
Summarize the MSStats results and data quantification	artmsMsstatsSummary
Generate Phosfate Input file	artmsPhosfateOutput
Generate PHOTON Input file	artmsPhotonOutput
Outputs a heatmap of the MSStats results created using the log2fold changes	artmsPlotHeatmapQuant
Converts the Protein ID column of the evidence file selected by the user to mod-site-specific notation: 'ProteinID' to 'ProteinID_AAnumber' notation	artmsProtein2SiteConversion
Quality Control analysis of the MaxQuant evidence file	artmsQualityControlEvidenceBasic
Extended Quality Control of the MaxQuant evidence.txt file	artmsQualityControlEvidenceExtended
Quality Control analysis of the evidence-like metabolomics dataset	artmsQualityControlMetabolomics
Quality Control of the MaxQuant summary.txt file	artmsQualityControlSummaryExtended
Relative quantification using MSstats	artmsQuantification
Reshape the MSstats results file from long to wide format	artmsResultsWide
Convert the SILAC evidence file to MSstats format	artmsSILACtoLong
Outputs the spectral counts from the MaxQuant evidence file.	artmsSpectralCounts
Volcano plot (log2fc / pvalues)	artmsVolcanoPlot
Write out a template file of the artMS configuration file (yaml)	artmsWriteConfigYamlFile

Package: artMS 1.31.0

artMS: Analytical R tools for Mass Spectrometry

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