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
mapReads2MDR            overlaps
mappingInfo             mappingInfo sequence analysis of contigs (for
                        SIMULATION only)
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
