Overview of the data instances | Overview of the data parameters | Basic instantiation | Advanced instantiation | Digging into the models | Tumor model | Sampling model | Sequencing noise model | Summary
Package: GeRnika 1.2.0
Aitor Sánchez-Ferrera
GeRnika: Simulation, Visualization and Comparison of Tumor Evolution Data
Simulating, visualizing and comparing tumor clonal data by using simple commands. This aims at providing a tool to help researchers to easily simulate tumor data and analyze the results of their approaches for studying the composition and the evolutionary history of tumors.
Authors:
GeRnika_1.2.0.tar.gz
GeRnika_1.2.0.tar.gz(r-4.7-any)GeRnika_1.2.0.tar.gz(r-4.6-any)
GeRnika_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GeRnika/json (API)
| # Install 'GeRnika' in R: |
| install.packages('GeRnika', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:5b23ffffc0. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 160 | ||
| source / vignettes | OK | 217 | ||
| linux-release-x86_64 | OK | 163 | ||
| wasm-release | OK | 142 |
Exports:add_noiseB_to_phylotreecombine_treescreate_Bcreate_Fcreate_instancecreate_phylotreecreate_Uequalsfind_common_subtreesplotplot_proportions
Dependencies:base64encbitbit64bslibcachemclicliprcolorspacecpp11crayondata.treeDiagrammeRdigestdplyrevaluatefarverfastmapfontawesomefsgenericsgluehighrhmshtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMatrixmemoisemimepillarpkgconfigplyrprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrreshape2rlangrmarkdownrstudioapisassscalesstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunyaml
Simulation of tumor clonal data (advanced users)
Last update: 2025-11-12
Started: 2024-09-05
Usage of GeRnika
Introduction | Simulating tumor clonal data | Topology parameter k | Simulate a tumor with k=0: | Simulate a tumor with k=1: | Create a Phylotree class object for each tumor: | Plot both trees | Sequencing noise | The Phylotree S4 class | Instantiation of Phylotree class objects | Comparing and combining phylogenetic trees | The equals method | The find_common_subtrees method | The combine_trees method | Session information
Last update: 2025-03-27
Started: 2024-09-05
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add noise to the VAF values in an F matrix | add_noise |
| A set of 10 trios of B matrices for experimenting with the methods of 'GeRnika' | B_mats |
| Create a 'Phylotree' object from a 'B' matrix. | B_to_phylotree |
| Get consensus tree between two phylogenetic trees | combine_trees |
| Create tumor phylogenetic tree topology | create_B |
| Calculate the variant allele frequency (VAF) values in a set of samples | create_F |
| Create a tumor phylogenetic tree instance | create_instance |
| Create a 'Phylotree' object | create_phylotree |
| Calculate tumor clone frequencies in samples | create_U |
| Check if two phylogenetic trees are equal | equals |
| Find the set of common subtrees between two phylogenetic trees | find_common_subtrees |
| Palettes for the methods of 'GeRnika' | palettes |
| S4 class to represent phylogenetic trees. | Phylotree-class |
| Plot a Phylotree object. | plot plot,Phylotree-method |
| Plot a phylogenetic tree with proportional node sizes and colors | plot_proportions |