Package: gmoviz 1.19.0
Kathleen Zeglinski
gmoviz: Seamless visualization of complex genomic variations in GMOs and edited cell lines
Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.
Authors:
gmoviz_1.19.0.tar.gz
gmoviz_1.19.0.zip(r-4.5)gmoviz_1.19.0.zip(r-4.4)gmoviz_1.19.0.zip(r-4.3)
gmoviz_1.19.0.tgz(r-4.4-any)gmoviz_1.19.0.tgz(r-4.3-any)
gmoviz_1.19.0.tar.gz(r-4.5-noble)gmoviz_1.19.0.tar.gz(r-4.4-noble)
gmoviz_1.19.0.tgz(r-4.4-emscripten)gmoviz_1.19.0.tgz(r-4.3-emscripten)
gmoviz.pdf |gmoviz.html✨
gmoviz/json (API)
NEWS
| # Install 'gmoviz' in R: |
| install.packages('gmoviz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- bright_colours_opaque - Gmoviz colour sets
- bright_colours_transparent - Gmoviz colour sets
- nice_colours - Gmoviz colour sets
- pastel_colours - Gmoviz colour sets
- rich_colours - Gmoviz colour sets
On BioConductor:gmoviz-1.19.0(bioc 3.21)gmoviz-1.18.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationsequencinggeneticvariabilitygenomicvariationcoverage
Last updated 26 days agofrom:f73a067779. Checks:OK: 5 NOTE: 2. 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 | OK | Nov 22 2024 |
| R-4.4-mac | OK | Nov 22 2024 |
| R-4.3-win | OK | Nov 22 2024 |
| R-4.3-mac | OK | Nov 22 2024 |
Exports:drawFeatureTrackdrawLinegraphTrackdrawScatterplotTrackfeatureDiagramgetCoveragegetFeaturesgetIdeogramDatagetLabelsgmovizInitialisegmovizPlotinsertionDiagrammakeLegendsmultipleInsertionDiagram
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIDelayedArraydigestdoParallelfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongGlobalOptionsgluegridBasehttrIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngpracmaR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsshapesnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc
gmoviz: seamless visualisation of complex genomic variations in GMOs and edited cell lines – Advanced usage
Rendered fromgmoviz_advanced.Rmdusingknitr::rmarkdownon Nov 22 2024.Last update: 2020-04-01
Started: 2020-02-17
gmoviz: seamless visualisation of complex genomic variations in GMOs and edited cell lines – An overview
Rendered fromgmoviz_overview.Rmdusingknitr::rmarkdownon Nov 22 2024.Last update: 2020-04-01
Started: 2020-01-31
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| gmoviz colour sets | bright_colours_opaque bright_colours_transparent colourSets nice_colours pastel_colours rich_colours |
| Add a 'feature' track to an existing plot | drawFeatureTrack |
| Add a line graph track to an existing plot | drawLinegraphTrack |
| Add a scatterplot track to an existing plot | drawScatterplotTrack |
| Display 'features' of interest in a diagram | featureDiagram |
| Import coverage data from .bam file | getCoverage |
| Generate a GRanges containing 'features' from .gff files | getFeatures |
| Import transgenic genome data from .bam or .fasta file | getIdeogramData |
| Generate a GRanges of labels from .gff files | getLabels |
| Initialise the layout of the circular plot | gmovizInitialise |
| Generate an entire circular plot | gmovizPlot |
| Display number of copies of an insertion | insertionDiagram |
| Add a legend | makeLegends |
| Display multiple insertion events around a genome | multipleInsertionDiagram |