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title: GAMBLR
url: https://github.com/morinlab/GAMBLR
template:
params:
bootswatch: flatly
ganalytics: UA-12345678-0
home:
sidebar:
structure: [links, license, community, citation, authors, dev]
links:
- text: Source Code
href: https://github.com/morinlab/GAMBLR
- text: Report A Bug
href: https://github.com/morinlab/GAMBLR/issues
- text: Insights
href: https://github.com/morinlab/GAMBLR/pulse
search:
reference:
- title: Annotations
desc: Functions used to annotate GAMBL data.
- contents:
- annotate_driver_ssm
- annotate_hotspots
- annotate_igh_breakpoints
- annotate_recurrent_cnv
- annotate_ssm_blacklist
- annotate_sv
- title: Bundled Data
desc: This is the bundled data used by GAMBLR.
- contents:
- chromosome_arms_grch37
- chromosome_arms_hg38
- dhitsig_genes_with_weights
- gene_blacklist
- grande_maf
- grch37_all_gene_coordinates
- grch37_gene_coordinates
- grch37_lymphoma_genes_bed
- grch37_oncogene
- grch37_partners
- hg38_gene_coordinates
- hg38_lymphoma_genes_bed
- hg38_oncogene
- hg38_partners
- hotspot_regions_grch37
- hotspot_regions_hg38
- lymphoma_genes_comprehensive
- reddy_genes
- target_regions_grch37
- target_regions_hg38
- wright_genes_with_weights
- title: cBioPortal
desc: Functions tailored to setting up a new study or updating an existing cBioPortal instance.
- contents:
- cbioportal_create
- custom_caselist
- finalize_study
- get_study_info
- setup_expreession_data
- setup_fusions
- setup_study
- study_check
- title: Checks
desc: GAMBLR functions that fall under the check category.
- contents:
- check_gambl_metadata
- check_gamblr_config
- check_host
- check_remote_configuration
- fread_maf
- title: Get Data
desc: A collection of functions used to retrieve data of different types.
- contents:
- get_ashm_count_matrix
- get_bams
- get_cn_segments
- get_cn_states
- get_coding_ssm
- get_coding_ssm_status
- get_combined_sv
- get_excluded_samples
- get_gambl_colours
- get_gambl_metadata
- get_gene_cn_and_expression
- get_gene_expression
- get_lymphgen
- get_manta_sv
- get_manta_sv_by_sample
- get_manta_sv_by_samples
- get_mutation_frequency_bin_matrix
- get_sample_cn_segments
- get_sample_wildcards
- get_samples_md5_hash
- get_ssh_session
- get_ssm_by_patients
- get_ssm_by_sample
- get_ssm_by_samples
- get_ssm_by_region
- get_ssm_by_regions
- title: Plotting
desc: Functions used for visualizing GAMBL data.
- contents:
- ashm_multi_rainbow_plot
- ashm_rainbow_plot
- calc_mutation_frequency_sliding_windows
- cnvKompare
- comp_report
- copy_number_vaf_plot
- fancy_alignment_plot
- fancy_circos_plot
- fancy_cnbar
- fancy_ideogram
- fancy_multisamp_ideogram
- fancy_propcov_plot
- fancy_proportions_plot
- fancy_qc_plot
- fancy_snv_chrdistplot
- fancy_sv_sizedens
- fancy_v_chrcount
- fancy_v_count
- fancy_v_sizedis
- focal_cn_plot
- FtestCNV
- plot_sample_circos
- prettyChromoplot
- prettyCoOncoplot
- prettyForestPlot
- prettyGeneCloud
- prettyOncoplot
- prettyRainfallPlot
- pretty_lollipop_plot
- splendidHeatmap
- theme_Morons
- title: Statistical testing and Computing
desc: Functions used for executing statistical and other calculations on incoming GAMBL data.
- contents:
- FtestCNV
- calc_mutation_frequency_sliding_windows
- calculate_pga
- cnvKompare
- count_ssm_by_region
- estimate_purity
- prettyForestPlot
- title: Utilities
desc: A collection of functions that fall under the utility category.
- contents:
- adjust_ploidy
- assemble_file_details
- assign_cn_to_ssm
- cleanup_maf
- consolidate_lymphgen
- collate_lymphgen
- collate_results
- fetch_output_files
- find_expected_outputs
- find_files_extract_wildcards
- gene_to_region
- genome_to_exome
- intersect_maf
- liftover_bedpe
- maf_to_custom_track
- make_igv_snapshot
- populate_each_tool_result
- populate_tool_results
- region_to_bins
- region_to_gene
- review_hotspots
- sanitize_maf_data
- sv_to_bedpe_file
- sv_to_custom_track
- supplement_maf
- tidy_gene_expression
- tidy_lymphgen
- view_mutation_igv
- write_sample_set_hash
navbar:
type: inverse
left:
- icon: fa-light fa-memo-circle-info
text: "How To"
menu:
- text: Install
href: https://morinlab.github.io/GAMBLR/#installation
- text: Running GAMBLR On Your Own Computer
href: https://morinlab.github.io/GAMBLR/#running-gamblr-on-your-own-computer
- text: Contribute
href: https://morinlab.github.io/GAMBLR/#contributing
- icon: fa-light fa-person-chalkboard
text: "Tutorials"
menu:
- text: SSM
href: articles/ssm_tutorial.html
- text: CN & SV
href: articles/cn_sv_tutorial.html
- text: Fancy Plots
href: articles/fancy_plots.html
- text: Utilities
href: articles/utilities_tutorial.html
right:
- icon: fa-file-code-o
text: "Functions & Bundled Data"
href: reference/index.html
- icon: fa-github fa-lg
text: "github"
href: https://github.com/morinlab/GAMBLR