r-bioc-genomicfeatures 1.16.3-1 / usr / lib / R / site-library / GenomicFeatures / NEWS

This file is indexed.

/usr/lib/R/site-library/GenomicFeatures/NEWS is in r-bioc-genomicfeatures 1.16.3-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  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
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
CHANGES IN VERSION 1.14
-----------------------

NEW FEATURES

    o keys method now has new arguments to allow for more
    sophisticated filtering.
    
    o adds genes() extractor 

    o makeTranscriptDbFromGFF() now handles even more different kinds
    of GFF files.


BUG FIXES

    o better argument checking for makeTranscriptDbFromGFF()

    o cols arguments and methods will now be columns arguments and methods



CHANGES IN VERSION 1.12
-----------------------

NEW FEATURES

    o Support for new UCSC species

    o Better support for GTF and GFF processing into TranscriptDb objects

    o Methods for making TranscriptDb objects from general sources
    have been made more useful


BUG FIXES

    o Updates to allow continued access to ever changing services like UCSC

    o Corrections for seqnameStyle methods

    o Over 10X performance gains for processing of GTF and GFF files


CHANGES IN VERSION 1.10
-----------------------

NEW FEATURES

    o Add makeTranscriptDbFromGFF().  Users can now use GFF files to
      make TranscriptDb resources.

    o Add *restricted* "seqinfo<-" method for TranscriptDb objects. It only
      supports replacement of the sequence names (for now), i.e., except for
      their sequence names, Seqinfo objects 'value' (supplied) and 'seqinfo(x)'
      (current) must be identical.

    o Add promoters() and getPromoterSeq().

    o Add 'reassign.ids' arg (FALSE by default) to makeTranscriptDb().

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated vignette.

    o Improve how makeTranscriptDbFromUCSC() and makeTranscriptDbFromBiomart()
      assign internal ids (see commit 65144 for the details).

    o 2.5x speedup of fiveUTRsByTranscript() and threeUTRsByTranscript().

DEPRECATED AND DEFUNCT

    o Are now defunct: transcripts_deprecated(), exons_deprecated(), and
      introns_deprecated().

    o Deprecate loadFeatures() and saveFeatures() in favor of loadDb() and
      saveDb(), respectively.

BUG FIXES

    o Better handling of BioMart data anomalies.

CHANGES IN VERSION 1.8
-----------------------

NEW FEATURES

    o Added asBED and asGFF methods to convert a TranscriptDb to a
      GRanges that describes transcript structures according to either
      the BED or GFF format. This enables passing a TranscriptDb
      object to rtracklayer::export directly, when targeting GFF/BED.

CHANGES IN VERSION 1.6
-----------------------

NEW FEATURES

    o TranscriptDbs are now available as standard packages.  Functions
    that were made available before the last release allow users to
    create these packages.

    o TranscriptDb objects now can be used with select

    o select method for TranscriptDb objects to extract data.frames of
    available annotations.  Users can specify keys, along with the
    keytype, and the columns of data that they want extracted from the
    annotation package.

    o keys now will operate on TranscriptDB objects to expose ID types
    as potential keys

    o keytypes will show which kinds of IDs can be used as a key by select

    o cols will display the kinds of data that can be extracted by select

    o isActiveSeq has been added to allow entire chromosomes to be
    toggled active/inactive by the user.  By default, everything is
    exposed, but if you wish you can now easily hide everything that
    you don't want to see.  Subsequence to this, all your accessors
    will behave as if only the "active" things are present in the
    database.

SIGNIFICANT USER-VISIBLE CHANGES

    o saveDb and loadDb are here and will be replacing saveFeatures
    and loadFeatures.  The reason for the name change is that they
    dispatch on (and should work with a wider range of object types
    than just trancriptDb objects (and their associated databases).

BUG FIXES

    o ORDER BY clause has been added to SQL statements to enforce more
    consistent ordering of returned rows.

    o bug fixes to enable DB construction to still work even after
    changes in schemas etc at UCSC, and ensembl sources.

    o bug fixes to makeFeatureDbFromUCSC allow it to work more
    reliably (it was being a little too optimistic about what UCSC
    would actually supply data for)

APT Browse - Built by Thomas Orozco.