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