CHANGES IN VERSION 1.56
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o goSlim() does not truncate Terms
(https://github.com/Bioconductor/GSEABase/issues/5)
CHANGES IN VERSION 1.54
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o orgDb no longer provide Unigene information. Remove support.
CHANGES IN VERSION 1.39
-----------------------
BUG FIXES
o goSlim() did not correctly count duplicate identifiers.
(https://support.bioconductor.org/p/100403/)
CHANGES IN VERSION 1.35
-----------------------
BUG FIXES
o some multi-line warnings and errors would fail without reporting
the error message.
o getGmt(), GO GeneSetCollection methods much faster.
CHANGES IN VERSION 1.31
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Support 'h' Broad set
BUG FIXES
o as(OBOCollection, "graphNEL") failed to include multiple
children
CHANGES IN VERSION 1.23
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Support 'c7' broad set
o Warn or remove duplicate geneIds when parsing GMT or Broad XML
CHANGES IN VERSION 1.21
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o GeneSetCollection,*,*,GOCollection-method respects evidenceCode
and ontology
CHANGES IN VERSION 1.19
-----------------------
NEW FEATURES
o Added UniprotIdentifier class
CHANGES IN VERSION 1.13
-----------------------
NEW FEATURES
o Parse Broad gene set sub-categories.
SIGNIFICANT USER-VISIBLE CHANGES
o An ad-hoc identifier replaces the Ruuid-based one.
CHANGES IN VERSION 1.5
----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Constructors for classes EntrezIdentifier, EnzymeIdentifier,
GenenameIdentifier, RefseqIdentifier, SymbolIdentifier,
UnigeneIdentifier can now accept an 'annotation' argument. This is
used to indicate which annotation package the identifiers are
from, e.g., EntrezIdentifier("hgu95av2.db") indicates that the
EntrezId's are from the hgu95av2.db package.
o GOCollection now tracks ontology as well as evidenceCode.
o Add ComputedCollection class to describe gene set collections
resulting from computations.
o Additional GeneSetCollection constructors
o Add OBOCollection class for reading OBO gene sets, including
functions to retrieve OBO collections from the internet
(getOBOCollectoin) and convert OBOCollections to and from graphNEL
objects.
o GeneSets constructed from GOCollections require a geneIdType
with an appropriate (i.e., GO to identifier) mapping, e.g.,
geneIdType=EntrezIdentifier("org.Hs.eg.db")
NEW FEATURES
o geneIdType<- and mapIdentifiers can now map between any two
identifier types within an annotation package, e.g.,
SymbolIdentifer('org.Hs.eg.db') to
GenenameIdentifier('org.Hs.eg.db')
o Parse revised Broad gene sets.
o More extensive information in some 'show' methods
o Added a mapIdentifiers method to allow maps with user-supplied
AnnDbBimap objects
BUG FIXES
o GO evidenceCodes updated to current codes available as defined
in GO
o GeneSetCollection,ExpressionSet,(Pfam|Prosite|Chrloc)Collection-method
now correctly navigate the underlying annotations and create gene
set collections
o A GeneSetCollection constructed with a named list could
incorrectly propagate the set names.
o Export MapCollection class
o Mapping AnnotationIdentifer to AnnotationIdentifier failed due
to incorrect method selection
(start date: 9 February, 2008)