Package: GeRnika 1.0.0

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:Aitor Sánchez-Ferrera [cre, aut], Maitena Tellaetxe-Abete [aut], Borja Calvo [aut]

GeRnika_1.0.0.tar.gz
GeRnika_1.0.0.tar.gz(r-4.5-noble)GeRnika_1.0.0.tar.gz(r-4.4-noble)
GeRnika_1.0.0.tgz(r-4.4-emscripten)GeRnika_1.0.0.tgz(r-4.3-emscripten)
GeRnika.pdf |GeRnika.html✨
GeRnika/json (API)

# Install 'GeRnika' in R:
install.packages('GeRnika', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • B_mats - A set of 10 trios of B matrices for experimenting with the methods of 'GeRnika'
  • hyperparameters - Hyperparameters for the methods of 'GeRnika'
  • palettes - Palettes for the methods of 'GeRnika'

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.00 score 157 downloads 15 exports 70 dependencies

Last updated 3 months agofrom:c6b0dedb26. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 04 2024
R-4.5-linuxOKDec 04 2024

Exports:.distribute_freqsadd_noiseB_to_phylotreecalc_clone_proportionscombine_treescreate_Bcreate_instancecreate_phylotreecreate_Uequalsfind_common_subtreesphylotree_to_Bplace_clones_spaceplotplot_proportions

Dependencies:base64encbitbit64bslibcachemclicliprcolorspacecpp11crayondata.treeDiagrammeRdigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsgluehighrhmshtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMatrixmemoisemimemunsellpillarpkgconfigplyrprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrreshape2rlangrmarkdownrstudioapisassscalesstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunyaml

Simulation of tumor clonal data (advanced users)

Aitor Sánchez, Maitena Tellaetxe and Borja Calvo

Rendered frommodels.Rmdusingknitr::rmarkdownon Dec 04 2024.

Last update: 2024-09-05
Started: 2024-09-05

Usage of GeRnika

Aitor Sánchez, Maitena Tellaetxe and Borja Calvo

Rendered fromusage.Rmdusingknitr::rmarkdownon Dec 04 2024.

Last update: 2024-09-05
Started: 2024-09-05

Readme and manuals

Help Manual

Help pageTopics
Distribute frequencies among clone and its children clones.distribute_freqs
Add noise to the VAF values in an F matrixadd_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
Calculate clone proportions for a tumorcalc_clone_proportions
Get consensus tree between two phylogenetic treescombine_trees
Create tumor phylogenetic tree topologycreate_B
Create a tumor phylogenetic tree instancecreate_instance
Create a 'Phylotree' objectcreate_phylotree
Calculate tumor clone frequencies in samplescreate_U
Check if two phylogenetic trees are equalequals
Find the set of common subtrees between two phylogenetic treesfind_common_subtrees
Retrieve the clone indices for a set of gene indicesget_clones
Retrieve the gene indices for the clones in a phylogenetic treeget_genes
Get parent nodes in a phylogenetic tree.get_parents
Hyperparameters for the methods of 'GeRnika'hyperparameters
S4 class to represent a node in a phylogenetic tree.Node-class
Palettes for the methods of 'GeRnika'palettes
Get B matrix from 'Phylotree' object.phylotree_to_B
Extract tree from 'Phylotree' object.phylotree_to_tree
S4 class to represent phylogenetic trees.Phylotree-class
Create a model for the spatial distribution of the clones in a tumorplace_clones_space
Plot a Phylotree object.plot plot,Phylotree-method
Plot a phylogenetic tree with proportional node sizes and colors.plot_p
Plot a phylogenetic treeplot_phylotree
Plot a phylogenetic tree with proportional node sizes and colorsplot_proportions