Table 2 isma user interface

pre_process

Read and integrate input files; generate unique identifiers

site_analysis

Perform site-level analyses, calling get_sites_statistics, overlap_Tools, overlap_Subjects

gene_analysis

Perform gene-level analyses, calling get_sites_statistics, overlap_Tools, overlap_Subjects, gene_mutation

site_annotation

Perform site annotation

integrate_TCGA

Integrate mutation evidence from TCGA

consensus_Tools

Calculate the consensus among tools

get_sites_statistics*

Calculate the co-occurrence of mutation sites/genes across callers and subjects

overlap_Subjects*

Calculate subject-by-subject site/gene co-occurrence matrix

overlap_Tools*

Calculate tool-by-tool site/gene co-occurrence matrix

ese_allsubj*

Calculate the variation of site/genes amount and show the results for each tool

ese_tool_subj*

Calculates the variation of site/genes amount, considering separately each tool and returns the results for each subject

ese_subj_tool*

Calculates the variation of site amount, considering separately each subject and returns the results for each caller

calculate_dist_to_exon

Calculate the site distance from the nearest exons

gene_mutation

Calculate the gene-by-subject mutation matrix and the gene mutation frequency vectors

filtering_sites

Filter sites