NEWS.md

In LieberInstitute/GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode

GenomicState 0.99.11

BUG FIXES

• GenomicState now requires derfinder version 1.21.7 or newer to fix a bug on derfinder::makeGenomicState() introduced by the change in R 4.0 on the default behavior of data.frame(stringsAsFactors = FALSE) which used to be TRUE. This error didn't break derfinder but was breaking gencode_genomic_state().

GenomicState 0.99.10

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://LieberInstitute.github.io/GenomicState/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

GenomicState 0.99.5

SIGNIFICANT USER-VISIBLE CHANGES

• The data is now live through AnnotationHub::AnnotationHub() and thus through GenomicStateHub(). The documentation now reflects this change.

GenomicState 0.99.2

SIGNIFICANT USER-VISIBLE CHANGES

• Addressed issues reported at http://bioconductor.org/spb_reports/GenomicState_buildreport_20191007121957.html
• Added the function GenomicStateHub() which will work once the data is uploaded to AnnotationHub.
• Edited the vignette links.

GenomicState 0.99.1

BUG FIXES

• Fixed some minor bugs.

GenomicState 0.99.0

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• Added the functions gencode_txdb(), gencode_annotated_genes() and gencode_genomic_state() for creating GenomicState objects from Gencode annotation files for human genome versions hg38 and hg19.
• Added local_metadata() for finding the data locally, particularly at JHPCE.

LieberInstitute/GenomicState documentation built on May 12, 2023, 5:15 p.m.