Tool documentation

The following tools have been implemented:

Perl tools

• gcoords2cons - Variation consequences
• gcoords2genes - Genes in the vicinity of a genomic coordinate
• gcoords2snp - Conversion of genomic coordinates to dbSNP IDs
• gcoords2ld - Linkage disequilibrium for genomic coordinate/gene pairs
• gcoords2reg - Retrieval of Ensembl regulatory information
• gene2canonexons - Extract exon coordinates of a Gene
• gcoordsconservation - Sequence conservation status/GERP scores retriever
• liftgcoords - Uplift genomic coordinates from past builds to current build
• snp2gcoords - Conversion of dbSNP IDs to genomic coordinates
• tbl2tbl - Text file to table converter.
• tblsubmerge - Merge previously split cells
• tblsubsplit - Split cells by a non-column separator character

Python tools

• ClinVarAnnotator - Retrieve information from ClinVar (NCBI)
• DMGeneIdConverter - Drosophila melanogaster gene ID converter
• DrugBankAnnotator - Furnish proteins with associated drugs
• GalaxyInstall - DIntegrator tools installation on Galaxy server
• GOAnnotator - Access Gene Onotology Annotation
• Gcoords2gcoords - Generation and split of genomic coordinates
• GOEnricher - Perform gene set enrichment analysis on sets of proteins.
• GOFunSim - Computes similarity between pairs of proteins.
• GOGraphBuilder - Generation of graphs furnished with annotation data
• HGMDAnnotator - Retrieve information from HGMD (Human Gene Mutation Database)
• HSEnsg2gcoords - Retrieve genomic coordinates for genes
• HSEnsgProteinMapper - Ensembl gene ID to protein ID mapping
• HSGeneAtlas - GNF Gene Atlas based gene expression assignment.
• HSGeneIdConverter - Homo sapiens gene ID converter
• HSGeneOrthologyMapper - Orthology mapping between human and a model organism
• InteractionAnnotator - Retrieve protein-protein interactions and co-complex data
• Interval2Genes - Finding genes in an interval
• MetaRanker - Combining multiple score columns into a single score
• MendelianFilter - VCF based filter for removing variants that do not comply with Mendelian inheritence.
• PharmaADMEntor - Flag variants reliably associated with drug metabolism
• Pos2LDBlock - Assignment of closest LD block for a location.
• Prioritizer - Utilizing Dintor modules for disease gene prioritization
• ReactomeAnnotator - Retrieve curated Reactome data
• SNPGeneGlobalLDChecker - Linkage disequilibrium block membership for genomic coordinates
• TableJoiner - Join two unsorted tables based on a common column
• VCF2Dint - Conversion from VCF to Dintor input format.