--- !ruby/object:Gem::Specification
name: pets
version: !ruby/object:Gem::Version
  version: 0.2.3
platform: ruby
authors:
- Elena Rojano, Pedro Seoane
autorequire:
bindir: bin
cert_chain: []
date: 2021-06-09 00:00:00.000000000 Z
dependencies:
- !ruby/object:Gem::Dependency
  name: bundler
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '2.0'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '2.0'
- !ruby/object:Gem::Dependency
  name: rake
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 13.0.3
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 13.0.3
- !ruby/object:Gem::Dependency
  name: rspec
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 3.10.0
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 3.10.0
- !ruby/object:Gem::Dependency
  name: statistics2
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: terminal-table
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: semtools
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 0.1.0
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 0.1.0
- !ruby/object:Gem::Dependency
  name: report_html
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: numo-narray
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: npy
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: parallel
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 1.20.1
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 1.20.1
description: PETS suite includes three different tools. CohortAnalyzer performs the
  calculation of several statistics that gives an overview of a cohort of patients
  to analyse. Reg2Phen uses associations between pathological phenotypes and regions
  of the genome (these associations can be calculated from the cohort of patients
  if they include genotypic & phenotypic information using NetAnalyzer, another Ruby
  gem) to find, for a given genomic region, which pathological phenotypes have been
  associated with that region. The third tool, Phen2Reg, is a predictor that using
  the same associations as Reg2Phen, predicts which genomic regions can be the cause
  of a list of pathological phenotypes observed in a patient.
email:
- elenarojano@uma.es, seoanezonjic@uma.es
executables:
- area_under_curve_pr.rb
- association_metrics_average.rb
- coPatReporter.rb
- comPatMondo.rb
- console
- evidence_profiler.rb
- fmeasure_index.rb
- generate_HPO_IC_table.rb
- get_PR_values.rb
- get_network_nodes.rb
- get_sorted_profs.rb
- merge_by_cluster.rb
- merge_pairs.rb
- paco_translator.rb
- phen2reg.rb
- phen2reg_predictor_check.rb
- profile_cleaner.rb
- reg2phen.rb
- region_to_patients_generator.rb
- relate_CI_to_association_value.rb
- setup
extensions: []
extra_rdoc_files: []
files:
- ".gitignore"
- ".rspec"
- ".travis.yml"
- Gemfile
- LICENSE.txt
- README.md
- Rakefile
- bin/area_under_curve_pr.rb
- bin/association_metrics_average.rb
- bin/coPatReporter.rb
- bin/comPatMondo.rb
- bin/console
- bin/evidence_profiler.rb
- bin/fmeasure_index.rb
- bin/generate_HPO_IC_table.rb
- bin/get_PR_values.rb
- bin/get_network_nodes.rb
- bin/get_sorted_profs.rb
- bin/merge_by_cluster.rb
- bin/merge_pairs.rb
- bin/paco_translator.rb
- bin/phen2reg.rb
- bin/phen2reg_predictor_check.rb
- bin/profile_cleaner.rb
- bin/reg2phen.rb
- bin/region_to_patients_generator.rb
- bin/relate_CI_to_association_value.rb
- bin/setup
- external_code/generate_boxpot.R
- external_code/get_clusters.R
- external_code/lines.R
- external_code/plot_area.R
- external_code/plot_boxplot.R
- external_code/plot_density.R
- external_code/plot_heatmap.R
- external_code/plot_scatterplot.R
- external_code/plot_scatterplot_simple.R
- external_code/ronto_plotter.R
- external_code/standardize_scores.R
- external_code/xyplot_graph.R
- external_data/biosystems_gene.gz
- external_data/bsid2info.gz
- external_data/chromosome_sizes_hg18.txt
- external_data/chromosome_sizes_hg19.txt
- external_data/chromosome_sizes_hg38.txt
- external_data/gene_data.gz
- external_data/gene_data_with_pathways.gz
- external_data/gene_location.gz
- external_data/hp.json
- external_data/hp.obo
- external_data/mondo.json
- external_data/mondo.obo
- external_data/remove
- external_data/uniq_hpo_with_CI.txt
- lib/pets.rb
- lib/pets/coPatReporterMethods.rb
- lib/pets/generalMethods.rb
- lib/pets/phen2reg_methods.rb
- lib/pets/reg2phen_methods.rb
- lib/pets/version.rb
- pets.gemspec
- templates/cluster_report.erb
- templates/cohort_report.erb
- templates/evidence_profile.erb
- templates/patient_report.erb
- templates/reg2phen_report.erb
- templates/similarity_matrix.erb
homepage: https://bitbucket.org/elenarojano/reg2phen/src/master/bin/reg2phen.rb
licenses:
- MIT
metadata: {}
post_install_message:
rdoc_options: []
require_paths:
- lib
required_ruby_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
required_rubygems_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
requirements: []
rubygems_version: 3.2.3
signing_key:
specification_version: 4
summary: Suite with predictive tools.
test_files: []