Mutational Significance in Cancer (Cancer Mutation Analysis) version 2.
Program: music2 - Mutational Significance in Cancer (Cancer Mutation Analysis) version 2.
Version: V0.1
Author: Beifang Niu && Cyriac Kandoth
Usage: music2 <command> [options]
Key commands:
bmr ... Calculate gene coverages and background mutation rates.
clinical-correlation Correlate phenotypic traits against mutated genes, or
against individual variants.
cosmic Match a list of variants to those in COSMIC, and highlight
druggable targets.
cosmic-omim Compare the amino acid changes of supplied mutations to
COSMIC and OMIM databases.
create-visualizations no description!!!: define doc in the class definition for
Genome::Model::Tools::Music::CreateVisualizations
data ... Parse, standardize, and index various third-party datasets
used by the tools in MuSiC.
mutation-relation Identify relationships of mutation concurrency or mutual
exclusivity in genes across cases.
path-scan Find signifcantly mutated pathways in a cohort given a list
of somatic mutations.
pfam Add Pfam annotation to a MAF file.
play Run the full suite of MuSiC tools sequentially.
plot ... Generate relevant plots and visualizations for MuSiC2.
proximity Perform a proximity analysis on a list of mutations.
proximity-window Perform a sliding window proximity analysis on a list of mutations.
smg Identify significantly mutated genes.
survival Create survival plots and P-values for clinical and mutational phenotypes.
Prerequisites:
Install samtools ( Download the samtools-0.1.19 from SOURCEFORGE (http://sourceforge.net/projects/samtools/files/samtools/0.1.19) )
tar jxf samtools-0.1.19.tar.bz2
cd samtools-0.1.19
make
export SAMDIR=$PWD
sudo mv samtools /usr/local/bin/
Install joinx
git clone --recursive https://github.com/genome/joinx.git
sudo apt-get install build-essential cmake libbz2-dev libgtest-dev
cd joinx
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=release
make deps
make
sudo make install
Install calcRoiCovg
sudo apt-get install git libbam-dev zlib1g-dev
git clone https://github.com/Beifang/calcRoiCovg.git
cd calc-roi-covg
make
sudo mv calcRoiCovg /usr/local/bin/
Install bedtools
curl http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz > BEDTools.tar.gz
tar -zxvf BEDTools.tar.gz
cd BEDTools-v2.17.0
make
sudo mv ./bin /usr/local/bin/
In order to install MuSiC2 package, we need CPANM program (cpanm - get, unpack build and install modules from CPANM)
sudo apt-get install cpanminus
Intall Perl5 local lib
cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
Intall Test::Most module
wget http://search.cpan.org/CPAN/authors/id/O/OV/OVID/Test-Most-0.34.tar.gz
cpanm Test-Most-0.34.tar.gz
Install MuSiC2 package
git clone https://github.com/ding-lab/MuSiC2
cd MuSiC2
cpanm MuSiC2-0.1.tar.gz
For user support please mail bniu@genome.wustl.edu