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_pkgdown.yml
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_pkgdown.yml
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destination: docs
template:
params:
footer: G. Caravagna, PhD.
url:
caravagnalab.github.io/CNAqc
repo:
url:
home: https://github.com/caravagnalab/CNAqc/
source: https://github.com/caravagnalab/CNAqc
issue: https://github.com/caravagnalab/CNAqc/issues
user: https://github.com/caravagnalab
authors:
Giulio Caravagna:
href: https://www.caravagnalab.org
reference:
- title: Available data
desc: References and datasets included in the package.
contents:
- chr_coordinates_hg19
- chr_coordinates_GRCh38
- example_dataset_CNAqc
- example_PCAWG
- fpr_test
- intogen_drivers
- gene_coordinates_hg19
- gene_coordinates_GRCh38
- title: Data processing
desc: Functions to manipulate and visualise the data.
contents:
- init
- Mutations
- CNA
- CNA_gene
- get_drivers
- plot_data_histogram
- plot_segments
- plot_segment_size_distribution
- plot_karyotypes
- plot_gw_counts
- plot_gw_depth
- plot_gw_vaf
- plot_icon_CNA
- plot_qc
- split_by_chromosome
- subsample
- subset_by_segment_karyotype
- subset_by_segment_totalcn
- subset_by_minimum_CCF
- subset_by_segment_minmutations
- subset_snvs
- print.cnaqc
- plot.cnaqc
- wt_mutant_alleles
- title: Purity and ploidy QC
desc: Analysis of calls by peak detection.
contents:
- analyze_peaks
- auto_tolerance
- inspect_segment
- plot_peaks_analysis
- get_PASS_percentage
- title: CCF estimation
desc: Computation of Cancer Cell Fractions data.
contents:
- compute_CCF
- CCF
- plot_CCF
- plot_gw_ccf
- title: Smoothing
desc: Analysis and plotting functions to smooth segments.
contents:
- smooth_segments
- plot_smoothing
- title: Overfragmentation detection
desc: Analysis and plotting functions to smooth segments.
contents:
- detect_arm_overfragmentation
- plot_arm_fragmentation
- title: Pipelines and parsers
desc: Pipelines and parsers implemented with CNAqc.
contents:
- Sequenza_CNAqc
- parse_Battenberg
- title: Variants annotation detection
desc: Annotation of putative variant drivers.
contents:
- annotate_variants
- title: Cohort functions
desc: Functions to visualise multiple objects at once.
contents:
- plot_multisample_CNA
- title: Mutational Signatures
desc: Functions to convert and store mutational signature tables
contents:
- SBS
- SBS_counts
- plot_SBS
- title: MAF interface
desc: Functions to convert from CNAqc to Maf format.
contents:
- as_maftools_obj
- as_maftools_cohort
- augment_with_maf
- augment_with_vep