Package: LipidomicsR 0.3.6
Hengyu Zhu
LipidomicsR: Elegant Tools for Processing and Visualization of Lipidomics Data
An elegant tool for processing and visualizing lipidomics data generated by mass spectrometry. 'LipidomicsR' simplifies channel and replicate handling while providing thorough lipid species annotation. Its visualization capabilities encompass principal components analysis plots, heatmaps, volcano plots, and radar plots, enabling concise data summarization and quality assessment. Additionally, it can generate bar plots and line plots to visualize the abundance of each lipid species.
Authors:
LipidomicsR_0.3.6.tar.gz
LipidomicsR_0.3.6.zip(r-4.5)LipidomicsR_0.3.6.zip(r-4.4)LipidomicsR_0.3.6.zip(r-4.3)
LipidomicsR_0.3.6.tgz(r-4.4-any)LipidomicsR_0.3.6.tgz(r-4.3-any)
LipidomicsR_0.3.6.tar.gz(r-4.5-noble)LipidomicsR_0.3.6.tar.gz(r-4.4-noble)
LipidomicsR_0.3.6.tgz(r-4.4-emscripten)LipidomicsR_0.3.6.tgz(r-4.3-emscripten)
LipidomicsR.pdf |LipidomicsR.html✨
LipidomicsR/json (API)
| # Install 'LipidomicsR' in R: |
| install.packages('LipidomicsR', repos = c('https://mingshi1.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mingshi1/lipidomicsr/issues
Last updated 7 months agofrom:8efb7db17d. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-win | NOTE | Nov 22 2024 |
| R-4.5-linux | NOTE | Nov 22 2024 |
| R-4.4-win | NOTE | Nov 22 2024 |
| R-4.4-mac | NOTE | Nov 22 2024 |
| R-4.3-win | OK | Nov 22 2024 |
| R-4.3-mac | OK | Nov 22 2024 |
Exports:abundance.lineplotabundance.plotabundance.signifabundance.summarychannel.deletedelRepFC_PgroupXpertheatmapimporternoridxnormalization_calculatorplotRadarQCplotreplicate.deletersd_calculatorsepclasstotal.abundancevolcano
Dependencies:abindaskpassbackportsbase64encbitbit64blobbootbroombslibcachemcallrcarcarDatacellrangerclassclicliprcodetoolscoincolorspaceconflictedcowplotcpp11crayoncurldata.tableDBIdbplyrDerivDescToolsdigestdoBydplyrdtplyre1071evaluateExactexpmfansifarverfastmapfmsbfontawesomeforcatsFormulafsgarglegenericsggforceggiraphggplot2ggplotifyggrepelggscigldgluegoogledrivegooglesheets4gridGraphicsgtablehavenhighrhmshtmltoolshtmlwidgetshttridsisobandjquerylibjsonliteknitrlabelinglatticelibcoinlifecyclelme4lmomlmtestlubridatemagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmodeltoolsmultcompmultcompViewmunsellmvtnormnlmenloptrnnetnortestnumDerivopensslpbkrtestpheatmappillarpkgconfigplyrpolyclipprettyunitsprocessxprogressproxypspurrrquantregR6raggrappdirsRColorBrewerrcompanionRcppRcppEigenreadrreadxlrematchrematch2reprexreshape2rlangrmarkdownrootSolverstudioapirvestsandwichsassscalesselectrSparseMstringistringrsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttidyversetimechangetinytextweenrtzdbutf8uuidvctrsviridisLitevroomwithrxfunxml2yamlyulab.utilszoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| absolute.calculator() | absolute.calculator |
| Plot Abundance Data | abundance.lineplot |
| Plot Abundance Data | abundance.plot |
| Analyze Abundance Significance | abundance.signif |
| Summarize Abundance Data | abundance.summary |
| Delete repeated channel data generated by LC-MS | channel.delete |
| delRep() | delRep |
| Calculate Fold Change and p-values for differential expression analysis | FC_P |
| groupXpert() | groupXpert |
| heatmap() | heatmap |
| importer() | importer |
| lEa() | lEa |
| lEr | lEr |
| Global environment settings of LipidomicsR | lipidomicsR_env |
| nor.absolute() | nor.absolute |
| nor.relative() | nor.relative |
| noridx() | noridx |
| normalization_calculator() | normalization_calculator |
| percent.calculator() | percent.calculator |
| plotRadar() | plotRadar |
| QCplot() | QCplot |
| relative.calculator() | relative_calculator |
| Delete repeated channel data generated by LC-MS | replicate.delete |
| Calculate Relative Standard Deviation (RSD) | rsd_calculator |
| sepclass() | sepclass |
| toGroup.calculator() | toGroup.calculator |
| Calculate Total Abundance Data | total.abundance |
| Generate Volcano Plot | volcano |
