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| addContigProperty | addContigProperty |
| addKOProperty | addKOProperty |
| adjacentPairs | Given a igraph object, adjacentPairs finds adjacent pairs of KOs |
| allTrios | Find all trios surrounding the KO of interest |
| annotateContigs.taxonomy | Adds taxonomic annotations of the contigs |
| blatting | blatting |
| buildTree | Taxonomic tree of the taxons |
| connect | Connecting to NEO4J Graph Database. |
| contigInfo | contigInfo |
| contractMetab | contractMetab shrinks a metabolic network's KOs into non-redundant units |
| cpdname | Finds the details of the CPD when given its ID |
| dbquery | Function for querying metamaps DB |
| findHomology | searches for KO's homology assignments |
| findNextKO | FindNextKO |
| findSeeds | To find all seed compounds in the metabolic graph |
| findTrios | findTrios searches valid three-KO reactions resticting by the center KO and reports reaction clusters |
| findtype | findType finds KOs/compounds ID in metabolic graph |
| grepgraph | Returns the metabolic graph given vector of KOs |
| grepgraph.cpd | Returns the metabolic graph given vector of KOs |
| ig2ggplot | Convert igraph to ggplot2 object |
| igraph2gexf | Converts igraph obj two gexf Function for converting igraph 2 gexf |
| index | Indexes the database for faster retrieval |
| ko2path | ko2path Finds all pathways related to the KO Finds all associated pathways, and returns a data.frame with ko and pathway details |
| koname | Gives KO details when supplied with KO id |
| lca | Finds the lowest common ancestor |
| listquery | Function for querying metamaps DB |
| lookupTable | generates 'lookupTable' for filtering raw data post gene centric assembly |
| map | map takes cDNA reads (fastQ format) and maps them onto contigs |
| mapContig | finds the location of the MDR on the contig |
| mappingInfo | mappingInfo sequence analysis of contigs (for SIMULATION only) |
| mapReads2MDR | overlaps |
| mdrRanges | Returns contig ranges for those captured within the MDR |
| nitrogenMetab | nitrogenMetab |
| path2kingdom | List all intermediaries between taxa and the superkingdom it belongs to |
| path2ko | Finds all KOs in a given pathway Finds all KOs belonging to a Pathways |
| pathways | List Pathways Lists all metabolic pathways |
| prettifyGraph | returns metabolic graph with all the ornaments set Adds details into the igraph object |
| scg | singleCopyGenes' |
| simpleThres | simpleThres |
| surrNODES | surrNODES finds nodes which are surrounding the given node |
| taxnam.sql | taxname.sql |
| taxname | Lists the taxonomic id's details |
| top500kos | Top500kos |