annotatr v1.1.12

• Documentation updates.

annotatr v1.1.11

• Add a function to build annotations from AnnotationHub resources, build_ah_annots().
• Change supported_annotations() and supported_genomes() into builtin_annotations() and builtin_genomes(). This enables more flexibility required for AnnotationHub annotations.
• Fix a bug in lncRNA annotation building caused by incomplete reference.

annotatr v1.1.10

• Update internal function documentation, specifically those functions related to HMM annotations. Want to avoid any WARNINGs in the builds.

NOTE: Builds of this release fail in Rdevel and Bioc 3.5, but is fine in R 3.3.z and Bioc 3.4.

annotatr v1.1.9

• Use rtracklayer::liftOver to lift FANTOM5 enhancers in hg19 and mm9 to h38 and mm10.
• Update documentation and vignette.

NOTE: Builds of this release fail in Rdevel and Bioc 3.5, but is fine in R 3.3.z and Bioc 3.4.

annotatr v1.1.8

• Require GenomeInfoDb >= 1.10.3

NOTE: Builds of this release fail in Rdevel and Bioc 3.5, but is fine in R 3.3.z and Bioc 3.4.

annotatr v1.1.7

• Change instances of scale_fill_brewer() to scale_fill_hue(). scale_fill_brewer() has a limit of 9 categories, and in many cases, this is too few.

annotatr v1.1.6

• supported_annotations() are now correctly given. In previous versions I mistakenly included CpG features for dm3 and dm6.
• Also included tests for building all supported_annotations().
• Comment out build_annotations() tests to save time on remote build environments.

annotatr v1.1.4

• Add chromHMM chromatin states for the 9 cell lines in hg19 for which they are available.
• Shortcut codes are of the form hg19_Gm12878-chromatin, and class codes are of the form hg19_chromatin_Gm12878-StrongEnhancer.
• Added tests and a blurb to the vignette.

annotatr v1.1.3

• Add support for CpG annotations for hg38, mm10, and rn6 via the UCSC goldenpath URLs.
  • Consequently, require readr as a dependency to get data from the URL.
  • Once these resources are added to AnnotationHub this method of retrieval will be removed.
• Minor vignette updates.