CHANGES IN VERSION 1.3.0 ------------------------ NEW FEATURES o Added quiet param to the queryEncode and searchEncode functions. o Added the Roadmap datasets. o Updated the encode_df object with the latest changes in the ENCODE. database. BUG FIXES o Solved a bug that caused get_schemas function to fail because a directory was added in the ENCODE database schemas. o Solved a bug with the searchEncode function caused by changes in the ENCODE REST API. CHANGES IN VERSION 1.5.0 ------------------------ NEW FEATURES o Updated clean_column to extract more information from ENCODE tables. o Deleted export_ENCODEdb_accession function. o Deleted update_ENCODEdb function. BUG FIXES o Solved various bug directly linked with the extraction of information from ENCODE database CHANGES IN VERSION 1.6.0 ------------------------ NEW FEATURES o Added fuzzySearch function, a less specific version of queryEncode o Added createDesign function to organize files extracted with queryEncode or fuzzySearch o New version of downloadEncode o Added the shinyApp of ENCODExplorer, see shinyEncode o Added a few column to encode_df database CHANGES IN VERSION 2.9.0 ------------------------ NEW FEATURES o The ENCODExplorer was split into 2 packages: ENCODExplorer and ENCODExplorerData o The encode_df object is now available through the AnnotationHub o The functions to interact with the ENCODExplorer API (except the search function) were moved to the ENCODExplorerData CHANGES IN VERSION 2.10.0 ------------------------ NEW FEATURES o Added the queryConsensusPeaks, queryGeneExpression and queryTranscriptExpression methods, along with buildConsensusPeaks and buildExpressionSummary. These methods allow the summarization of ENCODE ChIP-seq and RNA-seq results.