Package: CaMutQC 1.3.0
Xin Wang
CaMutQC: An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags. And a detailed and vivid filter report will be offered after completing a whole filtration or selection section. Also, CaMutQC integrates serveral methods and gene panels for Tumor Mutational Burden (TMB) estimation.
Authors:
CaMutQC_1.3.0.tar.gz
CaMutQC_1.3.0.zip(r-4.5)CaMutQC_1.3.0.zip(r-4.4)CaMutQC_1.3.0.zip(r-4.3)
CaMutQC_1.3.0.tgz(r-4.4-any)CaMutQC_1.3.0.tgz(r-4.3-any)
CaMutQC_1.3.0.tar.gz(r-4.5-noble)CaMutQC_1.3.0.tar.gz(r-4.4-noble)
CaMutQC_1.3.0.tgz(r-4.4-emscripten)CaMutQC_1.3.0.tgz(r-4.3-emscripten)
CaMutQC.pdf |CaMutQC.html✨
CaMutQC/json (API)
| # Install 'CaMutQC' in R: |
| install.packages('CaMutQC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/likelet/camutqc/issues
On BioConductor:CaMutQC-1.3.0(bioc 3.21)CaMutQC-1.2.0(bioc 3.20)
softwarequalitycontrolgenetargetcancer-genomicssomatic-mutations
Last updated 4 months agofrom:c466d6acc4. Checks:1 OK, 6 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | NOTE | Jan 28 2025 |
| R-4.4-mac | NOTE | Jan 28 2025 |
| R-4.3-win | NOTE | Jan 28 2025 |
| R-4.3-mac | NOTE | Jan 28 2025 |
Exports:calTMBmutFilterAdjmutFilterCanmutFilterCommutFilterDBmutFilterNormalDPmutFilterPONmutFilterQualmutFilterRefmutFilterRegmutFilterSBmutFilterTechmutFilterTypemutSelectionprocessMuttomaftoolstoMesKitvcfToMAF
Dependencies:AnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemcirclizecliclueclusterclusterProfilercodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDBIdigestDNAcopydoParallelDOSEdplyrDTenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGetoptLongggforceggfunggnewscaleggplot2ggplotifyggrepelggridgesggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgridGraphicsgsongtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemaftoolsmagrittrMASSMatrixmatrixStatsmclustmemoisememuseMesKitmgcvmimemunsellnlmeopensslorg.Hs.eg.dbpatchworkpermutephangornpheatmappillarpinfsc50pkgconfigplogrplyrpngpolyclippracmapromisespurrrquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenreshape2RhtslibrjsonrlangrmarkdownRSQLiteS4VectorssassscalesscatterpieshapesnowstringistringrsurvivalsyssystemfontstibbletidyrtidyselecttidytreetinytextreeiotweenrUCSC.utilsutf8vcfRvctrsveganviridisLitewithrxfunXVectoryamlyulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calTMB | calTMB |
| mutFilterAdj | mutFilterAdj |
| mutFilterCan | mutFilterCan |
| mutFilterCom | mutFilterCom |
| mutFilterDB | mutFilterDB |
| mutFilterNormalDP | mutFilterNormalDP |
| mutFilterPON | mutFilterPON |
| mutFilterQual | mutFilterQual |
| mutFilterRef | mutFilterRef |
| mutFilterReg | mutFilterReg |
| mutFilterSB | mutFilterSB |
| mutFilterTech | mutFilterTech |
| mutFilterType | mutFilterType |
| mutSelection | mutSelection |
| processMut | processMut |
| tomaftools | tomaftools |
| toMeskit | toMesKit |
| vcfToMAF | vcfToMAF |
