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Genome-Model-Tools-Music-0.04
River stage zero No dependents

Changes for version 0.04 - 2012-08-15

  • Implemented generalized linear models for regression analyses against clinical data
  • Added tools to generate typical visualizations like Kaplan-Meier survival estimates, and mutation status matrices
  • Support for TCGA Mutation Annotation Format (MAF) version 2.3
  • Performance improvements in mutation rate calculations, and more efficient memory usage
  • Added support for wiggle track format files describing coverage, if BAMs are unavailable

Modules

Genome::Model::Tools::Music::PathScan::CombinePvals
combining probabilities from independent tests of significance into a single aggregate figure
Genome::Model::Tools::Music::PathScan::PathScan
the Path-Scan significance test for mutations in groups of putative cancer genes
Genome::Model::Tools::Music::PathScan::PopulationPathScan
apply PathScan test to populations rather than just single individuals

Provides

Genome::Model::Tools::Music
in lib/Genome/Model/Tools/Music.pm
Genome::Model::Tools::Music::Base
in lib/Genome/Model/Tools/Music/Base.pm
Genome::Model::Tools::Music::Bmr
in lib/Genome/Model/Tools/Music/Bmr.pm
Genome::Model::Tools::Music::Bmr::Base
in lib/Genome/Model/Tools/Music/Bmr/Base.pm
Genome::Model::Tools::Music::Bmr::CalcBmr
in lib/Genome/Model/Tools/Music/Bmr/CalcBmr.pm
Genome::Model::Tools::Music::Bmr::CalcCovg
in lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm
Genome::Model::Tools::Music::Bmr::CalcCovgHelper
in lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm
Genome::Model::Tools::Music::Bmr::CalcWigCovg
in lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm
Genome::Model::Tools::Music::ClinicalCorrelation
in lib/Genome/Model/Tools/Music/ClinicalCorrelation.pm
Genome::Model::Tools::Music::CosmicOmim
in lib/Genome/Model/Tools/Music/CosmicOmim.pm
Genome::Model::Tools::Music::Galaxy
in lib/Genome/Model/Tools/Music/Galaxy.pm
Genome::Model::Tools::Music::MutationRelation
in lib/Genome/Model/Tools/Music/MutationRelation.pm
Genome::Model::Tools::Music::PathScan
in lib/Genome/Model/Tools/Music/PathScan.pm
Genome::Model::Tools::Music::Pfam
in lib/Genome/Model/Tools/Music/Pfam.pm
Genome::Model::Tools::Music::Play
in lib/Genome/Model/Tools/Music/Play.pm
Genome::Model::Tools::Music::Plot
in lib/Genome/Model/Tools/Music/Plot.pm
Genome::Model::Tools::Music::Plot::MutationRelation
in lib/Genome/Model/Tools/Music/Plot/MutationRelation.pm
Genome::Model::Tools::Music::Proximity
in lib/Genome/Model/Tools/Music/Proximity.pm
Genome::Model::Tools::Music::Smg
in lib/Genome/Model/Tools/Music/Smg.pm
Genome::Model::Tools::Music::Survival
in lib/Genome/Model/Tools/Music/Survival.pm

Other files