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_pkgdown.yml
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reference:
- title: "Core Data Structures"
desc: "Represent datasets and properties "
- subtitle: "Working with .mzrollDB experiments"
desc: "Connect to an mzrollDB sqlite database produced by MAVEN or quahog."
- contents:
- clamr
- mzroll_db_sqlite
- clamr_summary
- test_mzroll_db_con_schema
- validate_mzroll_db_schema
- mzroll_pass_bookmarks
- subtitle: "CLaM R Config"
desc: "Specify parameters tied to a mass spec experiment such as mass tolerances."
- contents:
- build_clamr_config
- clamr_config_assign
- format_mass_accuracy_input
- format_mass_accuracy_tolerances
- require_tolerances
- test_clamr_config
- subtitle: "Alternative Data Representations"
- contents:
- extract_peakset
- peakset_format_for_mzroll
- augment_peakgroups
- nest_peakgroup_features
- mz_set_example
- title: "Raw data workflows"
desc: "Interact with mass spec files rather than an .mzrollDB dataset"
- contents:
- tidy_mzR_from_msfile
- tidy_mzR_extract_mzs
- tidy_mzR_EICs
- tidy_mzR_plot_scans
- tidy_mzR_plot_major_features
- match_mzroll_db_to_file
- strip_ms_file_extension
- strip_ms_file_extension_from_extensions
- get_valid_ms_file_extensions
- ms2_scans_from_raw_files
- title: "Dataset-Level Transformation and Identification"
desc: "Update an experiment"
- subtitle: "Retention Time Alignment"
desc: "Align samples to correct for RT drift"
- contents:
- ms2_driven_aligner
- estimate_rt_drift
- estimate_mz_ppm_drift
- ms2_driven_aligner_plotting
- find_candidate_anchors
- update_sample_rt
- subtitle: "Coelution Detection"
desc: "Detect features which are related isotopologues or adducts"
- contents:
- identify_coelutions
- find_common_coelutions
- simplify_coelution_subgraph
- apply_coelution_labels
- generate_coelution_peaks
- combine_sample_coelutions_w_peaks
- peakgrp_coelution_annotation
- standard_coelution_library
- subtitle: "Detect Pathologies"
desc: "Identify complex noise"
- contents:
- identify_split_peaks
- smear_detection
- subtitle: "Dataset Filters"
desc: "Remove peakgroups or samples from a .mzrollDB experiment file"
- contents:
- find_unique_peakgroups
- merge_peakgroups
- remove_redundant_peakgroups
- reduce_mzroll_samples
- title: "Spectra"
desc: "Group, filter, and match spectra"
- contents:
- extract_fragments
- subtitle: "Grouping"
- contents:
- find_consistent_ms2_fingerprints
- group_similar_MS2
- score_fragmentation_similarity
- extract_and_group_fragments
- aggregate_scans
- sum_spectra
- subtitle: "Filtering"
- contents:
- spectra_filter_fragments
- filter_low_complexity_spectra
- filter_low_information_fragments
- title: "Utilities"
- subtitle: "Clustering"
desc: "Separate features into resolvable subsets"
- contents:
- find_mz_jumps
- find_scan_jumps
- find_density_minima
- subtitle: "Joins"
desc: "Join features by mass and retention time"
- contents:
- join_peaks_to_scans
- join_groupIds_to_mz_rts
- join_matching_standards
- match_peaksets
- mz_peak_join_fxn
- mz_scan_join_fxn
- subtitle: "Chemistry"
desc: "Work with chemical formulas"
- contents:
- parse_standard_formulas
- create_isotopic_chemical_formula
- estimate_chemical_formula
- split_formula
- formula_monoisotopic_mass
- adduct_mass
- isotope_summaries
- elemental_frequency_summary
template:
params:
bootswatch: flatly