Package: MSstatsLiP 1.13.0

Devon Kohler

MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

Authors:Devon Kohler [aut, cre], Tsung-Heng Tsai [aut], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Valentina Cappelletti [aut], Liliana Malinovska [aut], Olga Vitek [aut]

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MSstatsLiP.pdf |MSstatsLiP.html✨
MSstatsLiP/json (API)

# Install 'MSstatsLiP' in R:
install.packages('MSstatsLiP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/vitek-lab/msstatslip/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:MSstatsLiP-1.11.0(bioc 3.20)MSstatsLiP-1.10.0(bioc 3.19)

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrol

5.60 score 5 stars 5 scripts 188 downloads 18 exports 184 dependencies

Last updated 23 days agofrom:256206e81e. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 31 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:annotSitecalculateProteolyticResistancecalculateTrypticitycorrelationPlotLiPdataProcessPlotsLiPdataSummarizationLiPDIANNtoMSstatsLiPFormatgroupComparisonLiPgroupComparisonPlotsLiPlocateModlocatePTMPCAPlotLiPResistanceBarcodePlotLiPSkylinetoMSstatsLiPFormatSpectronauttoMSstatsLiPFormatStructuralBarcodePlotLiPtidyFastatrypticHistogramLiP

Dependencies:abindaskpassbackportsbase64encBiocGenericsBiostringsbitbit64bitopsblobbootbroombslibcachemcallrcarcarDatacaToolscellrangercheckmateclicliprclustercolorspaceconflictedcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdendextendDerivdigestdoBydplyrDTdtplyrellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeforcatsFormulafsgarglegenericsGenomeInfoDbGenomeInfoDbDataggplot2ggpubrggrepelggsciggsignifgluegoogledrivegooglesheets4gplotsgridExtragtablegtoolshavenhighrhmshtmltoolshtmlwidgetshttpuvhttridsIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleapslifecyclelimmalme4lmerTestlog4rlubridatemagrittrmarrayMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrMSstatsMSstatsConvertMSstatsPTMMSstatsTMTmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotlyplyrpolynompreprocessCoreprettyunitsprocessxprogresspromisespspurrrquantregR6raggrappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrematchrematch2reprexreshape2rlangrmarkdownrstatixrstudioapirvestS4Vectorssassscalesscatterplot3dselectrSparseMstatmodstringistringrsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytextzdbUCSC.utilsutf8uuidvctrsviridisviridisLitevroomwithrxfunxml2XVectoryamlzlibbioc

Proteolytic resistance analysis

Valentina Cappelletti ([email protected]), Malinovska Liliana ([email protected]), Devon Kohler ([email protected])

Rendered fromProteolytic_resistance_notebook.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-09-27
Started: 2022-04-18

MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package

Devon Kohler ([email protected])

Rendered fromMSstatsLiP_Workflow.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-09-27
Started: 2021-03-11

Readme and manuals

Help Manual

Help pageTopics
Annotate modification siteannotSite
Calcutates proteolytic resistance for provided data. Requires input from dataSummarizationLiP function. Can optionally calculate differential analysis using proteolytic resistance. In order for this function to work, Conditions and run numbers must match between the LiP and TrP data.calculateProteolyticResistance
Calculates level of trypticity for a list of LiP Peptides.calculateTrypticity
Plot run correlation for provided LiP and TrP experiment.correlationPlotLiP
Visualization for explanatory data analysisdataProcessPlotsLiP
Summarizes LiP and TrP datasets seperately using methods from MSstats.dataSummarizationLiP
Converts raw LiP MS data from DIA-NN into the format needed for MSstatsLiP.DIANNtoMSstatsLiPFormat
Model LiP and TrP data and make adjustments if needed Returns list of three modeled datasetsgroupComparisonLiP
Visualization for model-based analysis and summarizationgroupComparisonPlotsLiP
LiPRawDataLiPRawData
Locate modified sites with a peptidelocateMod
Annotate modified sites with associated peptideslocatePTM
MSstatsLiP: A package for identifying and analyzing changes in protein structures caused by compound binding in cellur lysates.MSstatsLiP
MSstatsLiP_dataMSstatsLiP_data
MSstatsLiP_modelMSstatsLiP_model
MSstatsLiP_SummarizedMSstatsLiP_Summarized
Visualize PCA analysis for LiP and TrP datasets.PCAPlotLiP
raw_lipraw_lip
raw_protraw_prot
Proteolytic Resistance Barcode plot. Shows accessibility score of different fully tryptic peptides in a protein.ResistanceBarcodePlotLiP
SkylineTestSkylineTest
Converts raw LiP MS data from Skyline into the format needed for MSstatsLiP.SkylinetoMSstatsLiPFormat
Converts raw LiP MS data from Spectronautt into the format needed for MSstatsLiP.SpectronauttoMSstatsLiPFormat
Barcode plot. Shows protein coverge of LiP modified peptides.StructuralBarcodePlotLiP
Read and tidy a FASTA filetidyFasta
TrPRawDataTrPRawData
Histogram of Half vs Fully tryptic peptides. Calculates proteotypicity, and then uses calcualtions in histogram.trypticHistogramLiP