/usr/lib/R/site-library/GenomeInfoDb/NEWS is in r-bioc-genomeinfodb 1.10.3-1.
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 | CHANGES IN VERSION 1.10.0
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NEW FEATURES
o Add function mapGenomeBuilds() that maps between UCSC and Ensembl
builds.
o Add function genomeBuilds() that list all the available UCSC or Ensembl
builds for a given organism[s] that can be used in mapGenomeBuilds()
o Add listOrganism() that list all currently available organism[s] included
for use in genomeBuilds()
DEPRECATED AND DEFUNCT
o After being deprecated, the species() method for GenomeDescription objects
is now defunct
MODIFICATIONS
o Zebra finch is removed as option for
fetchExtendedChromInfoFromUCSC() as it is not support yet
o keepStandardChromosomes() chooses first style when multiple are matched
BUG FIXES
o Fix WARNING occuring when determining style in keepStandardChromosomes()
CHANGES IN VERSION 0.99.7
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MODIFICATIONS
o rename:
isSupportedSeqnames -> .isSupportedSeqnames
supportedSeqnameStyles -> .supportedSeqnameStyles
supportedSeqnameMappings -> .supportedSeqnameMappings
isSupportedSeqnamesStyle -> .isSupportedSeqnamesStyle
CHANGES IN VERSION 0.99.6
----------------------------------
NEW FEATURES
o add new functions()
seqnamesInGroup which will take a character vector of chromosomes and
return the chromosomes specified by the group parameter supplied by the
user. The user can also give the species and the style.
seqnamesOrder() internally calls Herve's function makeSeqnameIds()
o add seqnameStyles generic and method from GenomicRanges
MODIFICATIONS
o rename:
testSeqnames -> isSupportedSeqnames
o move SeqnamesStyle generic from GenomicRanges and define a new method which
works on a character vector.
DEPRECATED AND DEFUNCT
o deprecate listAllSupportedStylesBySpecies(),
listAllSupportedSeqnameStyles(), supportedOrganisms()
supportedSeqnameMappingsWithGroup()
o deprecate supportedSeqnameMappings(), supportedSeqnameStyles(),
isSupportedSeqnamesStyle(),issupportedSeqnames()
CHANGES IN VERSION 0.99.17
----------------------------------
MODIFICATIONS
o keepStandardChromosomes: Make 'species' argument optional and remove
'style' argument.
CHANGES IN VERSION 0.99.14
----------------------------------
MODIFICATIONS
o rename:
package: Seqnames --> GenomeInfoDb
supportedStyles -> genomeStyles
makeSeqnameIds --> rankSeqlevels (add to export)
seqnamesOrder --> orderSeqlevels
extractSeqnameSet -> extractSeqlevels
extractSeqnameSetByGroup -> extractSeqlevelsByGroup
findSequenceRenamingMaps --> mapSeqlevels
seqnamesInGroup --> seqlevelsInGroup
seqnamesStyle --> seqlevelsStyle
"seqnameStyle<-" --> "seqlevelsStyle<-"
CHANGES IN VERSION 0.99.1
------------------------------
NEW FEATURES
o added new functions:
supportedOrganisms()
supportedSeqnameMappingsWithGroup()
extractSeqnameSetByGroup()
MODIFICATIONS
o The Seqnames package will have functions which will be moved from
AnnotationDbi , GenomicRanges
o List of 9 functions moved from AnnotationDbi
supportedSeqnameMappings, findSequenceRenamingMaps,
supportedSeqnameStyles, supportedSeqnames,
extractSeqnameSet, testSeqnames, isSupportedSeqnamesStyle,
listAllSupportedStylesBySpecies, listAllSupportedSeqnameStyles.
o makeSeqnameIds moved from GenomicRanges
o keepStandardChromosomes moved from GenomicRanges
o rename:
keepStandardChromosomes -> keepChromosomes
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