Package: ZygosityPredictor 1.5.0
Marco Rheinnecker
ZygosityPredictor: Package for prediction of zygosity for variants/genes in NGS data
The ZygosityPredictor allows to predict how many copies of a gene are affected by small variants. In addition to the basic calculations of the affected copy number of a variant, the Zygosity-Predictor can integrate the influence of several variants on a gene and ultimately make a statement if and how many wild-type copies of the gene are left. This information proves to be of particular use in the context of translational medicine. For example, in cancer genomes, the Zygosity-Predictor can address whether unmutated copies of tumor-suppressor genes are present. Beyond this, it is possible to make this statement for all genes of an organism. The Zygosity-Predictor was primarily developed to handle SNVs and INDELs (later addressed as small-variants) of somatic and germline origin. In order not to overlook severe effects outside of the small-variant context, it has been extended with the assessment of large scale deletions, which cause losses of whole genes or parts of them.
Authors:
ZygosityPredictor_1.5.0.tar.gz
ZygosityPredictor_1.5.0.zip(r-4.5)ZygosityPredictor_1.5.0.zip(r-4.4)ZygosityPredictor_1.5.0.zip(r-4.3)
ZygosityPredictor_1.5.0.tgz(r-4.4-any)ZygosityPredictor_1.5.0.tgz(r-4.3-any)
ZygosityPredictor_1.5.0.tar.gz(r-4.5-noble)ZygosityPredictor_1.5.0.tar.gz(r-4.4-noble)
ZygosityPredictor_1.5.0.tgz(r-4.4-emscripten)ZygosityPredictor_1.5.0.tgz(r-4.3-emscripten)
ZygosityPredictor.pdf |ZygosityPredictor.html✨
ZygosityPredictor/json (API)
NEWS
| # Install 'ZygosityPredictor' in R: |
| install.packages('ZygosityPredictor', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- GR_GENE_MODEL - Germline small variant object
- GR_GERM_SMALL_VARS - Germline small variant object
- GR_HAPLOBLOCKS - Haploblocks
- GR_SCNA - Copynumber object
- GR_SOM_SMALL_VARS - Somatic small variant object
On BioConductor:ZygosityPredictor-1.5.0(bioc 3.20)ZygosityPredictor-1.4.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:4445bbb19a
Exports:aff_germ_copiesaff_som_copiesgene_ovpredict_per_variantpredict_zygosityZP_ov
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicliprcodetoolscpp11crayoncurlDBIDelayedArraydplyrevaluatefansifastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehighrhmshttrigraphIRangesjsonliteKEGGRESTknitrlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6RCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8VariantAnnotationvctrsvroomwithrxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calculates how many copies are affected by a germnline small variant | aff_germ_copies |
| calculates how many copies are affected by a somatic small variant | aff_som_copies |
| accesor for gene predictions printing detailed info about how a gene status was assigned | gene_ov |
| germline small variant object | GR_GENE_MODEL |
| germline small variant object | GR_GERM_SMALL_VARS |
| haploblocks | GR_HAPLOBLOCKS |
| copynumber object | GR_SCNA |
| somatic small variant object | GR_SOM_SMALL_VARS |
| predicts zygosity of a set of variants | predict_per_variant |
| predicts zygosity of a set of genes of a sample | predict_zygosity |
| accesor for ZygoistyPredictor runs. Prints an overview about the run | ZP_ov |