/usr/lib/R/site-library/GenomeInfoDb/NEWS is in r-bioc-genomeinfodb 1.14.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
DEPRECATED AND DEFUNCT
o Remove 'force' argument from seqinfo() and seqlevels() setters (the
argument got deprecated in BioC 3.5 in favor of new and more flexible
'pruning.mode' argument).
BUG FIXES
o Add missing Y/chrY entry in seqlevel style db for Drosophila
melanogaster and Rattus norvegicus.
CHANGES IN VERSION 1.12.0
-------------------------
NEW FEATURES
o Add function standardChromosomes()
o Seqlevels() setter now supports "fine" and "tidy" modes on GRangesList and
GAlignmentsList objects
o Add assembly_accessions dataset
MODIFICATIONS
o Updated mapping table between UCSC and Ensembl to include recent builds
o Use https instead of http to fetch stuff from NCBI
o Replace 'force=TRUE' with 'pruning.mode="coarse"' in seqlevels() setter
o Add 'pruning.mode' argument to the keepSeqlevels(), dropSeqlevels(), and
keepStandardChromosomes() functions. IMPORTANT NOTE: Like for the
seqlevels() setter, the default pruning mode is "error", which means that
now these functions fail when some of the seqlevels to drop from 'x' are in
use. The old behavior was to silently prune 'x' (doing "coarse" pruning)
o Update files in data directory
o Updated internal functions .lookup_refseq_assembly_accession() and
fetch_assembly_report() for speed and efficiency
o move some files from GenomeInfoDb/data/ to GenomeInfoDbData annotation package
BUG FIXES
o fetch_assembly_summary() updated to work with recent changes to format of
files assembly_summary_genbank.txt and assembly_summary_refseq.txt
CHANGES IN VERSION 1.10.0
------------------------------
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
----------------------------------
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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