0. Load MSstatsTMT | 1. Converters for different peptide quantification tools | PDtoMSstatsTMTFormat() | Arguments | Example | MaxQtoMSstatsTMTFormat() | SpectroMinetoMSstatsTMTFormat() | OpenMStoMSstatsTMTFormat() | PhilosophertoMSstatsTMTFormat() | 2. Protein summarization, normalization and visualization | 2.1. proteinSummarization() | 2.2 dataProcessPlotsTMT() | 3. groupComparisonTMT()
Package: MSstatsTMT 2.21.2
Tony Wu
MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.
Authors:
MSstatsTMT_2.21.2.tar.gz
MSstatsTMT_2.21.2.zip(r-4.7-any)MSstatsTMT_2.21.2.zip(r-4.6-any)MSstatsTMT_2.21.2.zip(r-4.5-any)
MSstatsTMT_2.21.2.tgz(r-4.6-any)MSstatsTMT_2.21.2.tgz(r-4.5-any)
MSstatsTMT_2.21.2.tar.gz(r-4.7-any)MSstatsTMT_2.21.2.tar.gz(r-4.6-any)
MSstatsTMT_2.21.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MSstatsTMT/json (API)
| # Install 'MSstatsTMT' in R: |
| install.packages('MSstatsTMT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- input.pd - Example dataset in MSstatsTMT format.
On BioConductor:MSstatsTMT-2.21.1(bioc 3.24)MSstatsTMT-2.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologymassspectrometryproteomicssoftware
Last updated from:f49525e0ef. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 163 | ||
| linux-devel | NOTE | 332 | ||
| source / vignettes | OK | 240 | ||
| linux-release | NOTE | 291 | ||
| macos-release | NOTE | 163 | ||
| macos-oldrel | NOTE | 213 | ||
| windows-devel | NOTE | 187 | ||
| windows-release | NOTE | 194 | ||
| windows-oldrel | NOTE | 177 | ||
| wasm-release | OK | 122 |
Exports:dataProcessPlotsTMTdesignSampleSizeTMTgroupComparisonTMTMaxQtoMSstatsTMTFormatOpenMStoMSstatsTMTFormatPDtoMSstatsTMTFormatPhilosophertoMSstatsTMTFormatproteinSummarizationSpectroMinetoMSstatsTMTFormat
Dependencies:askpassbackportsbase64encbitopsbootbslibcachemcaToolscheckmateclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2ggrepelgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmalme4lmerTestmagrittrmarrayMASSMatrixmemoisemimeminqaMSstatsMSstatsConvertnlmenloptrnumDerivopensslotelpillarpkgconfigplotlypreprocessCorepromisespurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownS7sassscalesstatmodstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Visualization for explanatory data analysis - TMT experiment | dataProcessPlotsTMT |
| Planning future experimental designs of Tandem Mass Tag (TMT) experiments acquired with Data-Dependent Acquisition (DDA or shotgun) | designSampleSizeTMT |
| Finding differentially abundant proteins across conditions in TMT experiment | groupComparisonTMT |
| Example dataset in MSstatsTMT format. | input.pd |
| Summarizing peptide level quantification to protein level quantification | proteinSummarization |
