Version 0.15 • pipette

pipette 0.15.0 (2023-11-09)

Major changes:

export now supports list and S4Vectors List, for recursive export of supported objects. We may use this method in for other classes, such as SummarizedExperiment in AcidExperiment package in a future update.
export: GRangesList export method now inherits from List, and writes each object in list as a separate file to disk, rather than grouping in a data.frame coercion step first.

Minor changes:

export: GRangesList method is now defined and split out from data.frame method, to handle edge case of undesirable column name coercion.
Resolve new lints detected by lintr 3.1.1.

Minor changes:

import: Added support for Gene Ontology (GO) annotation files (GAF). Useful for importing data from the Gene Ontology Annotation (GOA) database.
Miscellaneous documentation improvements for import.

Major changes:

Updated dependencies to Bioconductor 3.18. These packages are now available on Bioconda.

Minor changes:

import: Reworked GAF file method to simply import as a 17 column data.frame. Refer to the Gene Ontology website for details on the GAF file format, which is basically a TSV files with commented lines beginning with "!".
Removed BaseSet as a suggested import. The getGAF function doesn’t work on most of the GAF files available from the Gene Ontology website currently. It only works reliably with the Homo sapiens protein annotations, which isn’t general enough for our needs currently.

Minor changes: