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