addContigProperty | addContigProperty |
addKOProperty | addKOProperty |
adjacentPairs | Given a igraph object, adjacentPairs finds adjacent pairs of... |
AllTrios | Find all trios surrounding the KO of interest |
annotateContigs.taxonomy | Adds taxonomic annotations of the contigs |
blatting | blatting |
buildE | buildE sorts the tree into a data.frame |
buildTree | buildTree - a taxonomic tree display function |
categorize | categorize |
connect | Connecting to NEO4J Graph Database. |
contigInfo | contigInfo |
contigsSurvive.repeats.readNum | contigsSurvive.repeats.readNum |
contigsSurvive.repeats.rpk | contigsSurvive.repeats.rpk |
contractMetab | contractMetab shrinks a metabolic network's KOs into... |
cpdname | Finds the details of the CPD when given its ID |
dbquery | Function for querying metamaps DB |
dollarpipe | with Pipe operator |
doublepipe | Double Pipe operator |
drawGradient | drawGradient gives the color gradient |
dynamicThreshold | dynamicThreshold tries to identify the lower bound converage... |
dynPlots | dynPlot Diagnostic plots |
extractFromPath | extractFromPath |
findHomology | searches for KO's homology assignments |
findK | findK to find the optimum number of Ks |
findNextKO | FindNextKO |
findPerl | findPerl finds the path to the executable |
findPython | findPython finds the path to the executable |
findSeeds | To find all seed compounds in the metabolic graph |
findTrios | findTrios searches valid three-KO reactions resticting by the... |
findtype | findType finds KOs/compounds ID in metabolic graph |
findV | findV finds the vertixID in the graph given its name |
gi2rank | gi2rank |
grep.cDNA | grep.cDNA |
grepgraph | Returns the metabolic graph given vector of KOs |
grepgraph_cpd | Generates metabolic network as IGRAPH object from input... |
grepgraph.cpd | Returns the metabolic graph given vector of KOs |
grepReads | grepReads greps for cDNA or gDNA reads cause they are both... |
ig2ggplot | Convert igraph to ggplot2 object |
igraph2gexf | Converts igraph obj two gexf Function for converting igraph 2... |
index | Indexes the database for faster retrieval |
ko2path | ko2path Finds all pathways related to the KO Finds all... |
koname | Gives KO details when supplied with KO id |
ksCal | ksCal generates KS statistics for aKO given the base... |
lca | Finds the lowest common ancestor |
listquery | Function for querying metamaps DB |
lookupTable | generates 'lookupTable' for filtering raw data post gene... |
make.data.frame | Convert columns with nested list structures into plain... |
map | map takes cDNA reads (fastQ format) and maps them onto... |
mapContig | finds the location of the MDR on the contig |
mappingInfo | mappingInfo sequence analysis of contigs (for SIMULATION... |
mapReads2MDR | overlaps |
mdrRanges | Returns contig ranges for those captured within the MDR |
nitrogenMetab | nitrogenMetab |
path2kingdom | List all intermediaries between taxa and the superkingdom it... |
path2ko | Finds all KOs in a given pathway Finds all KOs belonging to a... |
pathways | List Pathways Lists all metabolic pathways |
pipe | Pipe operator |
plotClassification | Plot clustering |
prettifyGraph | returns metabolic graph with all the ornaments set Adds... |
readStatusReader | readStatusReader stores read assignment details from the... |
rolling | rolling A dynamic threshold for the killing redundant contigs |
scg | singleCopyGenes' |
sigmaGraph | Takes mbgraph and outputs as a shinyApp Obj Users should... |
simpleThres | simpleThres |
simulated | finds all simulated genera for that particular KO |
surrNODES | surrNODES finds nodes which are surrounding the given node |
taxname | Lists the taxonomic id's details |
taxnam.sql | taxname.sql |
top500kos | Top500kos |
trio.local | trio.local |
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