NEWS

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chipenrich.data 2.16.0

• Transition to Kai Wang as maintainer.

chipenrich.data 2.10.0

• Added data required for proxReg: enhancers.dnase_thurman.0, gene.enh.desc, spline.log_dtss.90ENCODE
• Added mouse enhancer data for proxReg; added hg19 enhancer data to chipenrich.data

chipenrich.data 2.8.0

• Added Comparative Toxicogenomics Database for mm9

chipenrich.data 2.4.0

• Updated locus definitions based on TxDb 3.4.0 and OrgDb 3.5.0 packages
• Remove gene expression and EHMN gene sets.

chipenrich.data 2.2.0

• Updated GO gene sets based on org.Db and GO.db 3.4.2 packages.
• Added gene sets from MSigDB. Specifically Hallmark, Immunologic Signatures, MicroRNA targets, Oncogenic Signatures, and Transcription Factor targets for human.
• Added Comparative Toxicogenomics Database gene sets for human.
• Updated BioCarta, DrugBank, KEGG, and pfam gene sets for human.
• Use BioGrid for human protein interactions instead of MiMi.
• Remove mirBase and MiMi based gene sets.

chipenrich.data 2.0.0

NEW FEATURES

• Added locus definitions for danRer10 (zebrafish), dm6, hg38, rn5, and rn6.
• 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.
• Added Reactome genesets for fly.
• Added GO and Reactome genesets for zebrafish.

SIGNIFICANT USER-LEVEL CHANGES

• GO and Reactome gene sets are based on the most up to date data from orgDb and Reactome, respectively.
• Changes to LocusDefinition class.
• mcols for granges representation are 'gene_id' (formerly names) and 'symbol'
• Including gene symbols in the LocusDefinition allows removal of genes.*.RData
• Changes to tss.*.RData objects
• Now GRanges instead of a list with different representations.
• Use roxygen2 to build LocusDefinition, GeneSet, and tss documentation.
• Documentation for rebuilt objects in data/ include packages / sources used and version numbers.

SIGNIFICANT BACKEND CHANGES

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

DEPRECATED AND DEFUNCT

• Removed the chrom2iranges representation from the LocusDefinition class.

BUG FIXES

chipenrich.data 1.2.0

NEW FEATURES

• Support for D. melanogaster genome (dm3)
• All genomes (dm3, hg19, mm9, mm10, and rn4) have the following locus definitions
• 1kb, 5kb, 10kb, >10kb, introns, exons, nearest_gene, and nearest_tss
• New example histone data set, peaks_H3K4me3_GM12878, based on hg19.
• New gene sets from Reactome for human, mouse, and rat.

chipenrich.data 1.0

PKG FEATURES

• Supporting package containing data for use with the chipenrich package.
• Contains genesets for many databases including Biocarta, KEGG, OMIM, etc.
• Contains gene locus definitions (for assigning ChIP-seq peaks to genes)
• Contains mappability estimates for each gene locus definition
• Example ChIP-seq peak datasets

chipenrich.data 0.99.3

NEW FEATURES

• Locus definitions for mm10

BUG FIXES

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

chipenrich.data 0.99.2

USER-VISIBLE CHANGES

• Updated to switch from Depends: to Imports: per bioconductor guidelines
• Updated license to GPL-3
• Updated NEWS format per bioconductor guidelines
• Made several man pages runnable (removed donttest)

chipenrich.data 0.99.1

USER-VISIBLE CHANGES

• Minor updates to documentation and DESCRIPTION

chipenrich.data 0.99.0

NEW FEATURES

• Initial submission to bioconductor

chipenrich.data 0.4.4

USER-VISIBLE CHANGES

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

chipenrich.data 0.4.3

BUG FIXES

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

chipenrich.data 0.4.2

NEW FEATURES

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

BUG FIXES

• Fixed nearest gene mappabilities for human and mouse

chipenrich.data 0.4.1

USER-VISIBLE CHANGES

• Changed TSSs to come from knownGenes instead of refFlat

chipenrich.data 0.4

USER-VISIBLE CHANGES

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