CHANGES IN VERSION 2.16.0
-------------------------

    o Transition to Kai Wang as maintainer.

CHANGES IN VERSION 2.10.0
------------------------

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

    o Added mouse enhancer data for proxReg; added hg19 enhancer data to
      chipenrich.data

CHANGES IN VERSION 2.8.0
------------------------

    o Added Comparative Toxicogenomics Database for mm9

CHANGES IN VERSION 2.4.0
------------------------

    o Updated locus definitions based on TxDb 3.4.0 and OrgDb 3.5.0 packages

    o Remove gene expression and EHMN gene sets.

CHANGES IN VERSION 2.2.0
------------------------

    o Updated GO gene sets based on org.Db and GO.db 3.4.2 packages.

    o Added gene sets from MSigDB. Specifically Hallmark, Immunologic Signatures,
      MicroRNA targets, Oncogenic Signatures, and Transcription Factor targets
      for human.

    o Added Comparative Toxicogenomics Database gene sets for human.

    o Updated BioCarta, DrugBank, KEGG, and pfam gene sets for human.

    o Use BioGrid for human protein interactions instead of MiMi.

    o Remove mirBase and MiMi based gene sets.

CHANGES IN VERSION 2.0.0
------------------------

NEW FEATURES

    o Added locus definitions for danRer10 (zebrafish), dm6, hg38, rn5, and rn6.

    o 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.

    o Added Reactome genesets for fly.

    o Added GO and Reactome genesets for zebrafish.

SIGNIFICANT USER-LEVEL CHANGES

    o GO and Reactome gene sets are based on the most up to date data from orgDb
      and Reactome, respectively.

    o Changes to LocusDefinition class.

        o mcols for granges representation are 'gene_id' (formerly names) and 'symbol'

        o Including gene symbols in the LocusDefinition allows removal of genes.*.RData

    o Changes to tss.*.RData objects

        o Now GRanges instead of a list with different representations.

    o Use roxygen2 to build LocusDefinition, GeneSet, and tss documentation.

    o Documentation for rebuilt objects in data/ include packages / sources
      used and version numbers.

SIGNIFICANT BACKEND CHANGES

    o Use data-raw/ to store code for building LocusDefinition, GeneSet, and tss
      objects that are stored as RData in data/.

    o Use data-raw/ to store any data needed for GeneSet objects.

DEPRECATED AND DEFUNCT

    o Removed the chrom2iranges representation from the LocusDefinition class.

BUG FIXES

CHANGES IN VERSION 1.2.0
------------------------

NEW FEATURES

    o Support for D. melanogaster genome (dm3)

    o All genomes (dm3, hg19, mm9, mm10, and rn4) have the following locus definitions
      o 1kb, 5kb, 10kb, >10kb, introns, exons, nearest_gene, and nearest_tss

    o New example histone data set, peaks_H3K4me3_GM12878, based on hg19.

    o New gene sets from Reactome for human, mouse, and rat.

CHANGES IN VERSION 1.0
----------------------

PKG FEATURES

    o Supporting package containing data for use with the chipenrich package.

    o Contains genesets for many databases including Biocarta, KEGG, OMIM, etc.

    o Contains gene locus definitions (for assigning ChIP-seq peaks to genes)

    o Contains mappability estimates for each gene locus definition

    o Example ChIP-seq peak datasets

CHANGES IN VERSION 0.99.3
-------------------------

NEW FEATURES

    o Locus definitions for mm10

BUG FIXES

    o Mouse mappability gene IDs were incorrect for some locus definitions and
      would cause a crash if used

CHANGES IN VERSION 0.99.2
-------------------------

USER-VISIBLE CHANGES

    o Updated to switch from Depends: to Imports: per bioconductor guidelines

    o Updated license to GPL-3

    o Updated NEWS format per bioconductor guidelines

    o Made several man pages runnable (removed donttest)

CHANGES IN VERSION 0.99.1
-------------------------

USER-VISIBLE CHANGES

    o Minor updates to documentation and DESCRIPTION

CHANGES IN VERSION 0.99.0
-------------------------

NEW FEATURES

    o Initial submission to bioconductor

CHANGES IN VERSION 0.4.4
------------------------

USER-VISIBLE CHANGES

    o Updated 1kb/5kb locus definitions using new code

CHANGES IN VERSION 0.4.3
------------------------

BUG FIXES

    o Fixed 1kb/5kb locus definitions (they were previously the same by accident!)

CHANGES IN VERSION 0.4.2
------------------------

NEW FEATURES

    o Added support for rat (locus definitions, gene sets from GO and ConceptGen/LRpath)

BUG FIXES

    o Fixed nearest gene mappabilities for human and mouse

CHANGES IN VERSION 0.4.1
------------------------

USER-VISIBLE CHANGES

    o Changed TSSs to come from knownGenes instead of refFlat

CHANGES IN VERSION 0.4
----------------------

USER-VISIBLE CHANGES

    o Changed format of TSS object to include strand information
    o Updated cytoband to use Bioconductor (org.Mm.eg.db) for mouse