Version 0.4

AcidExperiment 0.4.0 (2022-05-04)

Major changes:

• Now requiring R 4.2 / Bioconductor 3.15.
• Lightened package by eliminating strong dependencies on scales, sessioninfo, and stringr package. Also removed dependency on tibble package via pipette.
• makeSummarizedExperiment will conditionally slot session_info from sessioninfo package if installed, otherwise will fall back to sessionInfo from utils package.

Minor changes:

• Reworking factor level support as droplevels2 instead of droplevels, to avoid method collisions with Bioconductor 3.15.
• Reformatted package code using styler conventions.

AcidExperiment 0.4.1 (2022-05-23)

Minor changes:

• Updated lintr checks and testthat unit tests.

AcidExperiment 0.4.2 (2022-05-25)

Minor changes:

• export: Hardened SummarizedExperiment against edge cases where no assays, colData, or rowData are defined.

AcidExperiment 0.4.3 (2022-06-02)

Minor changes:

• Hardened tempdir and unlink calls in unit tests and working examples, to improve compatibility in Windows testing environment.

AcidExperiment 0.4.4 (2022-10-25)

Major changes:

• export: Added initial method support for MultiAssayExperiment.

Minor changes:

• export: Hardened method to only use con, dropping support for legacy dir approach. These methods have been restricted based on the pending pipette v0.10 release series.
• Hardened dependencies to match Bioconductor 3.15 release series more clearly.

AcidExperiment 0.4.5 (2023-02-09)

Minor changes:

• Updated dependencies to Bioconductor 3.16.
• Migrated requireNamespaces import from AcidBase to goalie.

AcidExperiment 0.4.6 (2023-04-27)

Minor changes:

• Now consistently using DFrame instead of DataFrame; GRanges instead of GenomicRanges in S4 coercion and method definitions.
• Updated package to use new Ensembl2Ncbi and Ncbi2Ensembl generics now defined in AcidGenomes, instead of previous Ensembl2Entrez and Entrez2Ensembl. We are now using “NCBI” consistently across packages instead of the legacy “Entrez” name.