ENCODExplorer/NEWS at master · CharlesJB/ENCODExplorer · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
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.