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_pkgdown.yml
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_pkgdown.yml
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destination: docs
template:
params:
footer: S. Milite, L. Patruno, R. Bergamin and G. Caravagna.
url:
caravagnalab.github.io/Rcongas
repo:
url:
home: https://github.com/caravagnalab/Rcongas/
source: https://github.com/caravagnalab/Rcongas
issue: https://github.com/caravagnalab/Rcongas/issues
user: https://github.com/caravagnalab
authors:
Salvatore Milite:
href: https://www.caravagnalab.org
Lucrezia Patruno:
href: https://www.caravagnalab.org
Riccardo Bergamin:
href: https://www.caravagnalab.org
Giulio Caravagna:
href: https://www.caravagnalab.org
reference:
- title: Available data
desc: Data released with the package.
contents:
- multiome_congas_object
- metadata
- atac_counts
- rna_counts
- title: Main functions
desc: Functions to create and fit a dataset.
contents:
- create_congas_tibble
- init
- auto_config_run
- auto_normalisation_factor
- segments_selector_congas
- fit_congas
- title: Getters
desc: Functions to extract information from a model.
contents:
- get_input
- get_fit
- stat
- title: Filtering
desc: Functions to pre-process inputs and post-process models.
contents:
- filter_known_genes
- filter_counts_by_quantile
- filter_segments
- filter_outliers
- filter_missing_data
# * cap_values_by_quantile
# * filter_cells_by_quantile
# * filter_values_by_quantile
- title: Plotting functions
desc: Functions to plot data and fits.
contents:
- plot_data
- plot_fit
- title: S3 functions
desc: The `rcongasplus` S3 object functions.
contents:
- print.rcongasplus
- plot.rcongasplus
- title: Downstream analyses
desc: Functions to perform additional analyses downstream of the CONGAS+ inference.
contents:
- build_clone_tree
- title: internal
desc: Simulation functions
contents:
- change_spot
- create_df_from_range
- divide_genome_in_segments
- filter_cells_by_quantile
- generate_ploidy
- generate_ploidy_parent
- generate_ploidy_parent_fine
- generate_cluster_ploidy_df
- generate_random_tree
- hg38_karyo
- randomize_breaks
- run_simulation