import(igraph)
import(Matrix)
import(methods)
import(biom)

export(topologicalAnalyzeNet, checkMgrastMetagenome, listMgrastProject, differentialAnalyzeNet, constructMetabolicNetwork,
  delMgrastInbox, estimateAbundance, generateMgrastWebkey,
  generateMgrastWebsession, getKOPathwayInfo, getMgrastAnnotation,
  listMgrastInbox, loadMetabolicData, loginMgrast,
  preprocessKOMetabolites, saveMetabolicData, submitMgrastJob, 
  updateKEGGPathway, uploadMgrast, constructSSN, showMetagenomicNet)

importFrom(Biobase, isUnique, listLen)
importFrom(stringr, "str_sub<-", str_sub, str_extract_all, str_extract)
importFrom(plyr, laply, alply, d_ply, ldply, llply )
importFrom(ggplot2, ggplot, aes, aes_string, geom_point, stat_smooth, facet_wrap, scale_x_log10, scale_y_log10)
importFrom(reshape2, melt)
importFrom(RJSONIO, fromJSON, toJSON)
importFrom(KEGGREST, keggList, keggGet)
importFrom(RCurl, getURL, postForm, getForm, getCurlHandle, getCurlInfo, fileUpload, curlGlobalInit)
importFrom(XML, htmlParse, xmlDoc, xpathApply, getNodeSet, toString.XMLNode, xmlRoot, xmlSApply,   
  xmlAttrs, xmlChildren, xmlValue, xmlTreeParse)
importFrom(flexmix, KLdiv)
importFrom(tools, file_path_sans_ext)