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'))

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.

15 exports 0.00 score 70 dependencies

Last updated 13 days agofrom:c6b0dedb26. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-linux	OK	Sep 05 2024

Exports:.distribute_freqs add_noise B_to_phylotree calc_clone_proportions combine_trees create_B create_instance create_phylotree create_U equals find_common_subtrees phylotree_to_B place_clones_space plot plot_proportions

Dependencies:base64enc bit bit64 bslib cachem cli clipr colorspace cpp11 crayon data.tree DiagrammeR digest dplyr evaluate fansi farver fastmap fontawesome fs generics glue highr hms htmltools htmlwidgets igraph jquerylib jsonlite knitr labeling lattice lifecycle magrittr Matrix memoise mime munsell pillar pkgconfig plyr prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp readr reshape2 rlang rmarkdown rstudioapi sass scales stringi stringr tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite visNetwork vroom withr xfun yaml

Simulation of tumor clonal data (advanced users)

Aitor Sánchez, Maitena Tellaetxe and Borja Calvo

Rendered frommodels.Rmdusingknitr::rmarkdownon Sep 05 2024.

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

Usage of GeRnika

Aitor Sánchez, Maitena Tellaetxe and Borja Calvo

Rendered fromusage.Rmdusingknitr::rmarkdownon Sep 05 2024.

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

Citation

Readme and manuals

Help Manual

Help page	Topics
Distribute frequencies among clone and its children clones	.distribute_freqs
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
Calculate clone proportions for a tumor	calc_clone_proportions
Get consensus tree between two phylogenetic trees	combine_trees
Create tumor phylogenetic tree topology	create_B
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
Retrieve the clone indices for a set of gene indices	get_clones
Retrieve the gene indices for the clones in a phylogenetic tree	get_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 tumor	place_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 tree	plot_phylotree
Plot a phylogenetic tree with proportional node sizes and colors	plot_proportions