Genome-Model-Tools-Music

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

To install Genome::Model::Tools::Music, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Genome::Model::Tools::Music

CPAN shell

perl -MCPAN -e shell
install Genome::Model::Tools::Music

For more information on module installation, please visit the detailed CPAN module installation guide.

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Changes for version 0.04 - 2012-08-15

Modules

Provides

Other files

Module Install Instructions