Man pages for MetamapsDB
Network Analysis of Metabolic Pathways and Gene Based Assemblies in Metagenomics

addContigPropertyaddContigProperty
addKOPropertyaddKOProperty
adjacentPairsGiven a igraph object, adjacentPairs finds adjacent pairs of...
allTriosFind all trios surrounding the KO of interest
annotateContigs.taxonomyAdds taxonomic annotations of the contigs
blattingblatting
buildEbuildE sorts the tree into a data.frame
buildTreeTaxonomic tree of the taxons
categorizecategorize
connectConnecting to NEO4J Graph Database.
contigInfocontigInfo
contigsSurvive.repeats.readNumcontigsSurvive.repeats.readNum
contigsSurvive.repeats.rpkcontigsSurvive.repeats.rpk
contractMetabcontractMetab shrinks a metabolic network's KOs into...
cpdnameFinds the details of the CPD when given its ID
dbqueryFunction for querying metamaps DB
dollarpipewith Pipe operator
doublepipeDouble Pipe operator
dynamicThresholddynamicThreshold tries to identify the lower bound converage...
dynPlotsdynPlot Diagnostic plots
extractFromPathextractFromPath
findHomologysearches for KO's homology assignments
findKfindK to find the optimum number of Ks
findNextKOFindNextKO
findPerlfindPerl finds the path to the executable
findPythonfindPython finds the path to the executable
findSeedsTo find all seed compounds in the metabolic graph
findTriosfindTrios searches valid three-KO reactions resticting by the...
findtypefindType finds KOs/compounds ID in metabolic graph
findVfindV finds the vertixID in the graph given its name
grep.cDNAgrep.cDNA
grepgraphReturns the metabolic graph given vector of KOs
grepgraph_cpdGenerates metabolic network as IGRAPH object from input...
grepgraph.cpdReturns the metabolic graph given vector of KOs
grepReadsgrepReads greps for cDNA or gDNA reads cause they are both...
ig2ggplotConvert igraph to ggplot2 object
igraph2gexfConverts igraph obj two gexf Function for converting igraph 2...
indexIndexes the database for faster retrieval
ko2pathko2path Finds all pathways related to the KO Finds all...
konameGives KO details when supplied with KO id
ksCalksCal generates KS statistics for aKO given the base...
lcaFinds the lowest common ancestor
listqueryFunction for querying metamaps DB
lookupTablegenerates 'lookupTable' for filtering raw data post gene...
make.data.frameConvert columns with nested list structures into plain...
mapmap takes cDNA reads (fastQ format) and maps them onto...
mapContigfinds the location of the MDR on the contig
mappingInfomappingInfo sequence analysis of contigs (for SIMULATION...
mapReads2MDRoverlaps
mdrRangesReturns contig ranges for those captured within the MDR
nitrogenMetabnitrogenMetab
path2kingdomList all intermediaries between taxa and the superkingdom it...
path2koFinds all KOs in a given pathway Finds all KOs belonging to a...
pathwaysList Pathways Lists all metabolic pathways
pipePipe operator
plotClassificationPlot clustering
prettifyGraphreturns metabolic graph with all the ornaments set Adds...
readStatusReaderreadStatusReader stores read assignment details from the...
rollingrolling A dynamic threshold for the killing redundant contigs
scgsingleCopyGenes'
simpleThressimpleThres
simulatedfinds all simulated genera for that particular KO
surrNODESsurrNODES finds nodes which are surrounding the given node
taxnameLists the taxonomic id's details
taxnam.sqltaxname.sql
top500kosTop500kos
MetamapsDB documentation built on Dec. 6, 2017, 5:03 p.m.