1. Introduction | 1.1 Citation | 2. Prepare input Data | 2.1 MAF files | 2.2 Clinical data files | 2.3 CCF files | 2.4 Segmentation files | 3. Installation | Via Bioconductor | Via GitHub | 4. Start with the Maf object | 5. Mutational landscape | 5.1 Mutational profile | 5.2 CNA profile | 6. Measurement of intra-tumor heterogeneity | 6.1 Within tumors | 6.1.1 MATH score | 6.1.2 AUC of CCF | 6.1.3 Mutation clustering | 6.2 Between regions/tumors | 6.2.1 Fixation index | 6.2.2 Nei’s genetic distance | 7. Metastatic routes inference | 7.1 Pairwise CCF comparison | 7.2 Jaccard similarity index | 7.3 Neutral evolution | 8. Phylogenetic tree analysis | 8.1 Phylogenetic tree construction | 8.2 Compare Phylogenetic trees | 8.3 Functional exploration (custom module) | 8.4 Mutational characteristics analysis | 9. Phylogenetic tree visualization | 10. Shiny APP with video tutorial | 11. References | 12. Session Info
Package: MesKit 1.23.0
Mengni Liu
MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations
MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to depict mutational profiles, measure heterogeneity within or between tumors from the same patient, track evolutionary dynamics, as well as characterize mutational patterns on different levels. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the interpretation of tumor heterogeneity and the understanding of evolutionary relationship between regions in MRS study.
Authors:
MesKit_1.23.0.tar.gz
MesKit_1.23.0.zip(r-4.7)MesKit_1.23.0.zip(r-4.6)MesKit_1.23.0.zip(r-4.5)
MesKit_1.23.0.tgz(r-4.6-any)MesKit_1.23.0.tgz(r-4.5-any)
MesKit_1.23.0.tar.gz(r-4.7-any)MesKit_1.23.0.tar.gz(r-4.6-any)
MesKit_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MesKit/json (API)
| # Install 'MesKit' in R: |
| install.packages('MesKit', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:MesKit-1.23.0(bioc 3.24)MesKit-1.22.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:ee36e9486e. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 325 | ||
| linux-devel-x86_64 | WARNING | 625 | ||
| source / vignettes | OK | 460 | ||
| linux-release-x86_64 | WARNING | 676 | ||
| macos-release-arm64 | WARNING | 279 | ||
| macos-oldrel-arm64 | WARNING | 366 | ||
| windows-devel | WARNING | 806 | ||
| windows-release | WARNING | 840 | ||
| windows-oldrel | WARNING | 822 | ||
| wasm-release | OK | 337 |
Exports:calFstcalJSIcalNeiDistccfAUCclassifyMutcna2genecompareCCFcompareTreefitSignaturesgetBinaryMatrixgetBootstrapValuegetBranchTypegetCCFMatrixgetMafDatagetMafPatientgetMafRefgetMutBranchesgetNonSyn_vcgetPhyloTreegetPhyloTreePatientgetPhyloTreeRefgetPhyloTreeTsbLabelgetSampleInfogetTreegetTreeMethodmathScoremutClustermutHeatmapmutTrunkBranchplotCNAplotMutProfileplotMutSigProfileplotPhyloTreereadMafreadSegmentrunMesKitsubMaftestNeutraltriMatrix
Dependencies:AnnotationDbiapeaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncurldata.tableDBIdigestdoParalleldplyrfarverfastmapfastmatchforeachgenericsGetoptLongggplot2ggrepelggridgesGlobalOptionsgluegtablehttrigraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMatrixmatrixStatsmclustmemoisemimenlmeopensslphangornpillarpkgconfigpngpracmapurrrquadprogR6RColorBrewerRcpprjsonrlangRSQLiteS4VectorsS7scalesSeqinfoshapestringistringrsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calFst | calFst |
| compareJSI | calJSI |
| calNeiDist | calNeiDist |
| ccfAUC | ccfAUC |
| classifyMut | classifyMut |
| cna2gene | cna2gene |
| compareCCF | compareCCF |
| compareTree | compareTree |
| fitSignatures | fitSignatures |
| getBinaryMatrix | getBinaryMatrix getBinaryMatrix,phyloTree-method |
| getBootstrapValue | getBootstrapValue getBootstrapValue,phyloTree-method |
| getBranchType | getBranchType getBranchType,phyloTree-method |
| getCCFMatrix | getCCFMatrix getCCFMatrix,phyloTree-method |
| getMafData | getMafData getMafData,Maf-method |
| getMafPatient | getMafPatient getMafPatient,Maf-method |
| getMafRef | getMafRef getMafRef,Maf-method |
| getMutBranches | getMutBranches getMutBranches,phyloTree-method |
| getNonSyn_vc | getNonSyn_vc getNonSyn_vc,Maf-method |
| getPhyloTree | getPhyloTree |
| getPhyloTreePatient | getPhyloTreePatient getPhyloTreePatient,phyloTree-method |
| getPhyloTreeRef | getPhyloTreeRef getPhyloTreeRef,phyloTree-method getPhyloTreeTsbLabel,phyloTree-method |
| getPhyloTreeRef | getPhyloTreeTsbLabel |
| getSampleInfo | getSampleInfo getSampleInfo,Maf-method |
| getTree | getTree getTree,phyloTree-method |
| getTreeMethod | getTreeMethod getTreeMethod,phyloTree-method |
| Maf class | Maf Maf-class |
| MafList class | MafList MafList-class |
| mathScore | mathScore |
| mutCluster | mutCluster |
| mutHeatmap | mutHeatmap |
| mutTrunkBranch | mutTrunkBranch |
| phyloTree class | phyloTree phyloTree-class |
| phyloTreeList class | phyloTreeList-class |
| plotCNA | plotCNA |
| plotMutProfile | plotMutProfile |
| plotMutSigProfile | plotMutSigProfile |
| plotPhyloTree | plotPhyloTree |
| readMaf | readMaf |
| readSegment | readSegment |
| Run the default MesKit app for analysis locally | runMesKit |
| Subset Maf object | subMaf |
| testNeutral | testNeutral |
| triMatrix | triMatrix |
