makeGRangesFromGFFand other GFF utility functions, including
makeTx2geneFromGFF. Note that
makeGRangesFromGFFnow returns additional metadata columns accessible with
S4Vectors::mcols, and that these columns are now sorted alphabetically.
SummarizedExperiment class method support for
SummarizedExperiment. Previously, if
geneNamecolumn was a factor, this function would error. This issue has been fixed by ensuring that the symbols provided in
geneNameare coerced to a character vector.
SummarizedExperimentmethod support for converting objects containing gene symbols (“geneName”) as rownames back to gene identifiers (“geneID”).
eggnog: quickly download current annotations from EggNOG database. Useful for annotating gene-to-protein matches; currently in use with the brightworm RNAi screening package, which contains WormBase gene ID and EggNOG ID annotations.
dplyr::pullto reexported functions.
atomicas primary argument.
matchInterestingGroups: New developer function to automatically handle
interestingGroupsargument used across various plotting functions and in the bcbio infrastructure packges.