/usr/lib/R/site-library/AnnotationDbi/NEWS is in r-bioc-annotationdbi 1.40.0-1.
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The actual contents of the file can be viewed below.
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BUG FIXES
o fix bug in dbschema method for DBIConnection objects
o keys() no longer fails when global variable 'y' exists
CHANGES IN VERSION 1.34.0
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NEW FEATURES
o export ALIAS2EG symbol in NAMESPACE for frog, mosquito, chimp and
rhesus OrgDbs
o add how to use EnsDb section to vignette
MODIFICATIONS
o work on code base and exported functions
- break up code in geneCentricDbs file
- re-name and export functions used by select()
in AnnotationForge and GenomicFeatures
- re-name and export functions used by annotation package
builders in AnnotationForge
o remove library(RSQLite) from dbFileConnect()
o modify unit tests for new PFAM identifiers in Bioconductor 3.3
o use elementNROWS() instead of elementLengths()
o modify mapIds() to preserve data type returned from select()
o reduce time of AnnDbPkg-checker.Rd example
BUG FIXES
o bugfix for select() and mapIds() when there are many:many mappings
o bugfix in test_generateExtraRows unit test.
CHANGES IN VERSION 1.32.0
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BUG FIXES
o maps between chip and org packages work with loaded but not
attached packages.
CHANGES IN VERSION 1.31.0
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NEW FEATURES and API changes
o columns() and keytypes() sort their return values.
o ls() on a Bimap option returns keys in sort()ed order, by default
CHANGES IN VERSION 1.30.0
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NEW FEATURES and API changes
o Adds mapIds() which allows users who miss mget() to extract data
from AnnnotationDb objects: but without the dangers of using mget()
(which fails if you pass in a bad key)
o Adds dbconn() and dbfile() methods to the list of things that
AnnotationDb derived objects shoould always be expected to support
BUG FIXES AND CODE MAINTENANCE
o loadDb() now is smarter about whether or not it attaches a supporting
package
CHANGES IN VERSION 1.24.0
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NEW FEATURES and API changes
o keys method now has new arguments to allow for more
sophisticated filtering.
o cols method is now the columns method to make for a more
constistent interface.
o cols argument is now the columns argument (for select) to also
make the interface consistent across all use cases
BUG FIXES AND CODE MAINTENANCE
o better argument checking for select and related methods
o keys that end with ' will no longer cause grief except to
hapless life scientists who will still have to wonder who in their
right mind thinks it's a good idea for a gene symbol to be the
same except end with a 'prime'.
CHANGES IN VERSION 1.22.0
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NEW FEATURES
o There is now a convenience function for extracting data from
the GO.db package as a graph object. The function is called:
makeGOGraph.
o Adds supportedSeqnameMappings() and findSequenceRenamingMaps()
utilities.
o Improved vignette for new users
BUG FIXES AND CODE MAINTENANCE
o Fixes a bug in select for users accessing reactome.db
o Fixes a bug in select for users requesting via a PROBEID
o Fixes a bug in select for users using rat chip packages
o Fixes a bug in mget, for Bimap objects (when ifnotfound=NA)
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* *
* 1.20.x SERIES NEWS *
* *
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CHANGES IN AnnotationDbi VERSION 1.20.x
NEW FEATURES
o There is a new introductory vignette for AnnotationDbi. It
explains how to use the new simplified select method interface and
also describes how developers can implement their own select
interfaces for exposing new annotation resources.
o select support has been added for both the inparanoid and
reactome.db packages. These are in addition to existing support
for all ChipDb, OrgDb, and TranscriptDb packages. GO.db also has
a select interface.
o Code has been added to enhance backwards compatibility between
select and bimaps. The aim here is that old code that uses bimaps
should still work with packages that have the same kind of data
exposed using only a select() interface.
SIGNIFICANT USER-VISIBLE CHANGES
o AnnotationDbi has been split up and simplified. All code needed
for building and supporting new packages has been moved to a new
package called AnnotationForge. The remaining code is what is
needed to support day-to-day interaction with the Annotation
interface.
BUG FIXES AND CODE MAINTENANCE
o The code for generating bimaps has been simplified and overhauled.
o The code for making manual pages in annotation packages has been
simplified so that there will be far less redundancy
o The select(), cols, keys, and keytypes methods saw several bug
fixes and a code overhaul to enhance both speed and reliablity.
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* *
* 1.16.x SERIES NEWS *
* *
**************************************************
CHANGES IN AnnotationDbi VERSION 1.16
NEW FEATURES
o New Object types: Org.Db, ChipDb, GODb. These are loaded when
an Annotation package is loaded.
o select method for these new 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 new objects to expose most ID types as 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 Users who need organism packages for organisms that are
annotated at NCBI can now use makeOrgPackageFromNCBI() to generate
a basic organism package on the fly
SIGNIFICANT USER-VISIBLE CHANGES
o New objects are always named after the package that loaded them.
So if you just loaded the hgu95av2.db package, your ChipDb object
will be called hgu95av2.db
o new fields are now required in the metadata table of annotation
packages to allow the on-the-fly creation of these new objects.
If you are constructing a custom package and want to extend this
infrastructure, you may need to add some fields to the metadata
table.
BUG FIXES
o makeProbePackage, and other generated Annotation packages have
had templates modified so that packages can load and also to
enable loading of new objects to allow new features in this
release.
o updated GOFrame constructor to allow use of new types of
evidence codes.
o generated packages will create databases with the appropiate
metadata entries for the new objects.
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* *
* 1.9.x SERIES NEWS *
* *
**************************************************
CHANGES IN AnnotationDbi VERSION 1.9.5
NEW FEATURES
o An organism package has been added for Streptomyces coelicolor
o extensive overhaul of inparanoid packages means that inparanoid
packages now match to 100 different organisms
o Extended support for ensembl mappings to yeast and flies.
NOTEWORTHY CHANGES BETWEEN THIS version and 1.3.11
o All chip packages now depend on org packages. This simplifies
the schema and also allows for more convenient updating of these
packages and smaller downloads for users.
o chip package mappings that contain probes which map to multiple
targets are now hidden by default, with the ability to be exposed
when required. See the use of the new toggleProbes() method.
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* *
* 1.3.11 SERIES NEWS *
* *
**************************************************
CHANGES IN AnnotationDbi VERSION 1.3.11
NEW FEATURES
o Support has been added for 3 more organisms, this means that the
current list of supported organisms as of 1.3.11 is the following:
Arabidopsis thaliana
Bos taurus
Caenorhabditis elegans
Canis familiaris
Drosophila melanogaster
Danio rerio
Escherichia coli K12 Strain
Escherichia coli Sakai Strain
Gallus gallus
Homo sapiens
Mus musculus
Plasmodium falciparum
Rattus norvegicus
Saccharomyces cerevisiae
Sus scrofa
o Added support for GO to canine and pig packages by using
BLAST2GO (this data was not available from NCBI for these
organisms).
o ZFIN IDs are supported for Zebrafish packages.
o Wormbase IDs are supported for C. elegans packages.
o Uniprot IDs have been added to almost all package types.
o CHRLOCEND mapping has been added which give gene end positions
for almost all packages and compliments the CHRLOC mapping which
already provides the start positions.
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* *
* 1.3.9 SERIES NEWS *
* *
**************************************************
CHANGES IN AnnotationDbi VERSION 1.3.9
NEW FEATURES
o Support added for Malaria, Zebrafish, two strains of E coli,
bovine and canine.
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* *
* 1.1.7 SERIES NEWS *
* *
**************************************************
CHANGES IN AnnotationDbi VERSION 1.1.7
NEW FEATURES
o Annotation packages now have a function to display basic
quality control information.
o 5 Inparanoid packages have been added for use in studies
involving homology.
o Ensembl gene ID maps have been added to all mammalian
packages.
o MGI IDs maps have been added for all Mouse packages.
o Protein to gene mappings have been added to appropriate
organism based packages so that it will be possible to get
from the IDs in the inparanoid packages to a gene based ID
for the 5 main organism types (ie. Human, Mouse, Rat, Fly,
Yeast).
o Support has been added for PFAM so that there can now be a
PFAM.db package.
o AnnotationDbi is now compliant with the 1.0 schema definition.
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