Version: 2.16.0
Text: Transition to Kai Wang as maintainer.

Version: 2.10.0
Text: Added data required for proxReg: enhancers.dnase_thurman.0,
        gene.enh.desc, spline.log_dtss.90ENCODE

Version: 2.10.0
Text: Added mouse enhancer data for proxReg; added hg19 enhancer data
        to chipenrich.data

Version: 2.8.0
Text: Added Comparative Toxicogenomics Database for mm9

Version: 2.4.0
Text: Updated locus definitions based on TxDb 3.4.0 and OrgDb 3.5.0
        packages

Version: 2.4.0
Text: Remove gene expression and EHMN gene sets.

Version: 2.2.0
Text: Updated GO gene sets based on org.Db and GO.db 3.4.2 packages.

Version: 2.2.0
Text: Added gene sets from MSigDB. Specifically Hallmark, Immunologic
        Signatures, MicroRNA targets, Oncogenic Signatures, and
        Transcription Factor targets for human.

Version: 2.2.0
Text: Added Comparative Toxicogenomics Database gene sets for human.

Version: 2.2.0
Text: Updated BioCarta, DrugBank, KEGG, and pfam gene sets for human.

Version: 2.2.0
Text: Use BioGrid for human protein interactions instead of MiMi.

Version: 2.2.0
Text: Remove mirBase and MiMi based gene sets.

Version: 2.0.0
Category: NEW FEATURES
Text: Added locus definitions for danRer10 (zebrafish), dm6, hg38, rn5,
        and rn6.

Version: 2.0.0
Category: NEW FEATURES
Text: All genomes have the following locus definitions: nearest_tss,
        nearest_gene, exon, intron, 1kb, 5kb, 10kb,
        1kb_outside_upstream, 5kb_outside_upstream,
        10kb_outside_upstream, 1kb_outside, 5kb_outside, and
        10kb_outside.

Version: 2.0.0
Category: NEW FEATURES
Text: Added Reactome genesets for fly.

Version: 2.0.0
Category: NEW FEATURES
Text: Added GO and Reactome genesets for zebrafish.

Version: 2.0.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: GO and Reactome gene sets are based on the most up to date data
        from orgDb and Reactome, respectively.

Version: 2.0.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: Changes to LocusDefinition class.

Version: 2.0.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: mcols for granges representation are 'gene_id' (formerly names)
        and 'symbol'

Version: 2.0.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: Including gene symbols in the LocusDefinition allows removal of
        genes.*.RData

Version: 2.0.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: Changes to tss.*.RData objects

Version: 2.0.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: Now GRanges instead of a list with different representations.

Version: 2.0.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: Use roxygen2 to build LocusDefinition, GeneSet, and tss
        documentation.

Version: 2.0.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: Documentation for rebuilt objects in data/ include packages /
        sources used and version numbers.

Version: 2.0.0
Category: SIGNIFICANT BACKEND CHANGES
Text: Use data-raw/ to store code for building LocusDefinition,
        GeneSet, and tss objects that are stored as RData in data/.

Version: 2.0.0
Category: SIGNIFICANT BACKEND CHANGES
Text: Use data-raw/ to store any data needed for GeneSet objects.

Version: 2.0.0
Category: DEPRECATED AND DEFUNCT
Text: Removed the chrom2iranges representation from the LocusDefinition
        class.

Version: 2.0.0
Category: BUG FIXES
Text:

Version: 1.2.0
Category: NEW FEATURES
Text: Support for D. melanogaster genome (dm3)

Version: 1.2.0
Category: NEW FEATURES
Text: All genomes (dm3, hg19, mm9, mm10, and rn4) have the following
        locus definitions

Version: 1.2.0
Category: NEW FEATURES
Text: 1kb, 5kb, 10kb, >10kb, introns, exons, nearest_gene, and
        nearest_tss

Version: 1.2.0
Category: NEW FEATURES
Text: New example histone data set, peaks_H3K4me3_GM12878, based on
        hg19.

Version: 1.2.0
Category: NEW FEATURES
Text: New gene sets from Reactome for human, mouse, and rat.

Version: 1.0
Category: PKG FEATURES
Text: Supporting package containing data for use with the chipenrich
        package.

Version: 1.0
Category: PKG FEATURES
Text: Contains genesets for many databases including Biocarta, KEGG,
        OMIM, etc.

Version: 1.0
Category: PKG FEATURES
Text: Contains gene locus definitions (for assigning ChIP-seq peaks to
        genes)

Version: 1.0
Category: PKG FEATURES
Text: Contains mappability estimates for each gene locus definition

Version: 1.0
Category: PKG FEATURES
Text: Example ChIP-seq peak datasets

Version: 0.99.3
Category: NEW FEATURES
Text: Locus definitions for mm10

Version: 0.99.3
Category: BUG FIXES
Text: Mouse mappability gene IDs were incorrect for some locus
        definitions and would cause a crash if used

Version: 0.99.2
Category: USER-VISIBLE CHANGES
Text: Updated to switch from Depends: to Imports: per bioconductor
        guidelines

Version: 0.99.2
Category: USER-VISIBLE CHANGES
Text: Updated license to GPL-3

Version: 0.99.2
Category: USER-VISIBLE CHANGES
Text: Updated NEWS format per bioconductor guidelines

Version: 0.99.2
Category: USER-VISIBLE CHANGES
Text: Made several man pages runnable (removed donttest)

Version: 0.99.1
Category: USER-VISIBLE CHANGES
Text: Minor updates to documentation and DESCRIPTION

Version: 0.99.0
Category: NEW FEATURES
Text: Initial submission to bioconductor

Version: 0.4.4
Category: USER-VISIBLE CHANGES
Text: Updated 1kb/5kb locus definitions using new code

Version: 0.4.3
Category: BUG FIXES
Text: Fixed 1kb/5kb locus definitions (they were previously the same by
        accident!)

Version: 0.4.2
Category: NEW FEATURES
Text: Added support for rat (locus definitions, gene sets from GO and
        ConceptGen/LRpath)

Version: 0.4.2
Category: BUG FIXES
Text: Fixed nearest gene mappabilities for human and mouse

Version: 0.4.1
Category: USER-VISIBLE CHANGES
Text: Changed TSSs to come from knownGenes instead of refFlat

Version: 0.4
Category: USER-VISIBLE CHANGES
Text: Changed format of TSS object to include strand information

Version: 0.4
Category: USER-VISIBLE CHANGES
Text: Updated cytoband to use Bioconductor (org.Mm.eg.db) for mouse