Man Pages in
libgenome-model-tools-music-perl
Carta.tech
Packages
libgenome-model-tools-music-perl
36
Section 1p:
Executable programs or shell commands
genome-music.1p
Mutational significance in cancer (cancer mutation analysis)
genome-music-bmr.1p
Calculate gene coverages and background mutation rates.
genome-music-bmr-calc-bmr.1p
Calculates mutation rates given per-gene coverage (from "music bmr calc-covg"), and a mutation list
genome-music-bmr-calc-covg.1p
Uses calcroicovg.c to count covered bases per-gene for each given tumor-normal pair of bams.
genome-music-bmr-calc-covg-helper.1p
Uses calcroicovg.c to count covered bases per-gene for a tumor-normal pair of bams.
genome-music-bmr-calc-wig-covg.1p
Count covered bases per-gene for each given wiggle track format file.
genome-music-clinical-correlation.1p
Correlate phenotypic traits against mutated genes, or against individual variants
genome-music-cosmic-omim.1p
Compare the amino acid changes of supplied mutations to cosmic and omim databases.
genome-music-galaxy.1p
Run the full suite of music tools sequentially.
genome-music-mutation-relation.1p
Identify relationships of mutation concurrency or mutual exclusivity in genes across cases.
genome-music-path-scan.1p
Find signifcantly mutated pathways in a cohort given a list of somatic mutations.
genome-music-pfam.1p
Add pfam annotation to a maf file
genome-music-play.1p
Run the full suite of music tools sequentially.
genome-music-plot.1p
Generate relevant plots and visualizations for music.
genome-music-plot-mutation-relation.1p
Makes plots for results from the mutation-relation tool
genome-music-proximity.1p
Perform a proximity analysis on a list of mutations.
genome-music-smg.1p
Identify significantly mutated genes.
genome-music-survival.1p
Create survival plots and p-values for clinical and mutational phenotypes.
gmt-music.1p
Mutational significance in cancer (cancer mutation analysis)
gmt-music-bmr.1p
Calculate gene coverages and background mutation rates.
gmt-music-bmr-calc-bmr.1p
Calculates mutation rates given per-gene coverage (from "music bmr calc-covg"), and a mutation list
gmt-music-bmr-calc-covg.1p
Uses calcroicovg.c to count covered bases per-gene for each given tumor-normal pair of bams.
gmt-music-bmr-calc-covg-helper.1p
Uses calcroicovg.c to count covered bases per-gene for a tumor-normal pair of bams.
gmt-music-bmr-calc-wig-covg.1p
Count covered bases per-gene for each given wiggle track format file.
gmt-music-clinical-correlation.1p
Correlate phenotypic traits against mutated genes, or against individual variants
gmt-music-cosmic-omim.1p
Compare the amino acid changes of supplied mutations to cosmic and omim databases.
gmt-music-galaxy.1p
Run the full suite of music tools sequentially.
gmt-music-mutation-relation.1p
Identify relationships of mutation concurrency or mutual exclusivity in genes across cases.
gmt-music-path-scan.1p
Find signifcantly mutated pathways in a cohort given a list of somatic mutations.
gmt-music-pfam.1p
Add pfam annotation to a maf file
gmt-music-play.1p
Run the full suite of music tools sequentially.
gmt-music-plot.1p
Generate relevant plots and visualizations for music.
gmt-music-plot-mutation-relation.1p
Makes plots for results from the mutation-relation tool
gmt-music-proximity.1p
Perform a proximity analysis on a list of mutations.
gmt-music-smg.1p
Identify significantly mutated genes.
gmt-music-survival.1p
Create survival plots and p-values for clinical and mutational phenotypes.
4
Section 3pm:
Library calls
Genome::Model::Tools::Music::PathScan::CombinePvals.3pm
Combining probabilities from independent tests of significance into a single aggregate figure
Genome::Model::Tools::Music::PathScan::PathScan.3pm
The path-scan significance test for mutations in groups of putative cancer genes
Genome::Model::Tools::Music::PathScan::PopulationPathScan.3pm
Apply pathscan test to populations rather than just single individuals
Genome::Model::Tools::Music::Proximity.3pm
None