Version 0.3

AcidSingleCell 0.3.0 (2022-05-05)

Major changes:

• Now requiring R 4.2 / Bioconductor 3.15.
• S4 classes that contain DataFrame were updated to inherit DFrame instead, due to a breaking change in Bioconductor 3.15.

Minor changes:

• Reformatted package code using styler conventions.
• metrics: Removed tbl_df return option, to remove dependency on tibble package, in favor of simply using Bioconductor S4Vectors.
• Removed strong dependency on stringr in favor of stringi package.
• Removed dependency on scales package, by removing percent usage in filterCells reporting statistics.

AcidSingleCell 0.3.1 (2022-05-24)

Minor changes:

• Updated lintr checks and testthat unit tests.

AcidSingleCell 0.3.2 (2022-06-02)

Minor changes:

• Hardened temporary file handling in working examples and unit tests, to improve Windows compatibility.

AcidSingleCell 0.3.3 (2022-10-25)

Major changes:

• export: Reduced the number of exported methods, matching the conventions in updated pipette v0.10.0 package. Note that con is now required instead of dir for target directory.

Minor changes:

• diffExpPerCluster and findMarkers: Made the CLI messages less busy by calling alert instead of h1 internally.
• geometricMean and zerosVsDepth: Reworked method to dispatch on sparseMatrix instead of Matrix, due to breaking changes in Matrix 1.5 release. Note that coercion to logical Matrix should now be used calling lMatrix instead of lgCMatrix. See zerosVsDepth for details.

AcidSingleCell 0.3.4 (2023-02-09)

Minor changes:

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

AcidSingleCell 0.3.5 (2023-04-27)

Minor changes:

• Updated NAMESPACE for compatibility with Bioconductor 3.17.
• Now classing on DFrame directly instead of DataFrame virtual class.

AcidSingleCell 0.3.6 (2023-08-17)

Minor changes:

• diffExp: Remove references to BiocParallel, which are now picked up automatically in DESeq2.
• Now requiring R 4.3 / Bioconductor 3.17.
• Updated lintr checks.