NAMESPACE

importFrom('seqinr',
           write.fasta)

importFrom('yaml',
           as.yaml,
           yaml.load_file)

importFrom('gplots',
           heatmap.2,
           colorpanel)

importFrom('mclust',
           Mclust,
           mclust2Dplot,
           mclustBIC)

exportClasses(cobindr, configuration, SeqObj)

exportMethods(detrending,
              find.pairs, get.bindingsite.ranges,
              plot.detrending,
              plot.gc,
              plot.pairdistance,
              plot.positionprofile,
              plot.positions,
              plot.positions.simple,
              plot.tfbs.heatmap,
              plot.tfbs.venndiagram,
              plot.tfbslogo,
              predicted2pwm,
              rtfbs, search.gadem, search.pwm,
              testCpG,
              write.bindingsites,
              write.bindingsites.table,
              get.pairs,
              write.sequences,
              get.significant.pairs,
uid, name, sequences, bg_sequences, desc, configuration,
 pfm, binding_sites, bg_binding_sites, pairs, bg_pairs, 
pairs_of_interest, species, location, comment, sequence,
 experiment_description, id, sequence_source, 
sequence_origin, sequence_type, bg_sequence_source, 
bg_sequence_type, bg_sequence_origin, downstream, 
upstream, max_distance, pairs, pfm_path, threshold, 
fdrThreshold, path, mart, pseudocount, pValue)

exportPattern("*.<-")

export(read.transfac.pfm,
       generate.background,
		cobindr, seqObj, cobindRConfiguration)

# Import all packages listed as Imports or Depends
import(
  biomaRt,
  methods,
  gmp,
  Biostrings,
  BSgenome,
  rtfbs,
  IRanges
)