graphite/NAMESPACE at master · sales-lab/graphite · GitHub

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# Copyright 2011-2023 Gabriele Sales <gabriele.sales@unipd.it>
#
#
# This file is part of graphite.
#
# graphite is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License
# version 3 as published by the Free Software Foundation.
#
# graphite is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public
# License along with graphite. If not, see <http://www.gnu.org/licenses/>.

importFrom(AnnotationDbi, columns, mapIds)
importFrom(httr, GET, http_status, write_disk)
importFrom(methods, is, new)
importFrom(rappdirs, user_cache_dir)
importFrom(stats, na.omit)
importFrom(utils, download.file, getFromNamespace, installed.packages)

importMethodsFrom(graph,
  edgeData, "edgeData<-", "edgeDataDefaults<-", edges, nodeData, "nodeData<-",
  nodes)

importFrom(graphics, plot)


exportClasses(Pathways, PathwayList, Pathway)


# Re-exports
exportMethods(edgeData, "edgeData<-", "edgeDataDefaults<-", edges, nodes)

exportMethods(
  convertIdentifiers, plot,
  prepareSPIA, runTopologyGSA)

export(
  pathways, pathwayDatabases, pathwayId, pathwayTitle, pathwayDatabase,
  pathwaySpecies, pathwayTimestamp, pathwayURL, buildPathway, cytoscapePlot,
  pathwayGraph, runSPIA)

S3method(as.list, PathwayList)