NEWS.md

In acidgenomics/r-acidsinglecell: Acid Genomics Single Cell Experiment

Release notes

AcidSingleCell 0.4.2 (2024-03-27)

Minor changes:

• importCellCycleMarkers, importCellTypeMarkers: reworked internal code to no longer use makeGeneToSymbolFromEnsembl, which is slated to be removed in the next AcidGenomes package update. Instead it is recommended to use makeGRangesFromEnsembl to generate a GRanges object first, and then generate GeneToSymbol in a secondary call.
• Added code coverage for CellCycleMarkers and CellTypeMarkers generators.
• Improved factor handling in CellCycleMarkers and CellTypeMarkers output.

AcidSingleCell 0.4.1 (2023-10-27)

Minor changes:

• Migrated indropsSampleIndexCounts from koopa R package here.
• Updated some internal leftJoin steps to ensure we don't type switch.

AcidSingleCell 0.4.0 (2023-10-04)

Major changes:

• Now enforcing strict camel case in all function names.
• Renamed convertSampleIDsToNames to convertSampleIdsToNames.

Minor changes:

• Updated unit tests to reflect changes in AcidTest package update.

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.

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 0.3.4 (2023-02-09)

Minor changes:

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

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 0.3.2 (2022-06-02)

Minor changes:

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

AcidSingleCell 0.3.1 (2022-05-24)

Minor changes:

• Updated lintr checks and testthat unit tests.

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 0.2.0 (2022-03-11)

Significantly reworked the package, migrating some single-cell RNA-seq analysis code that was previously defined in pointilllism package, but is generally applicable for any type of single-cell RNA-seq. We are reworking the pointillism package to function primarily as an extension toolkit for Seurat and monocle3.

New functions and classes:

• Migrated barcodeRanksPerSample, cellCountsPerCluster, cpm, diffExp, diffExpPerCluster, findMarkers, and normalize methods that dispatch on SingleCellExperiment here from pointillism.
• Migrated CellCycleMarkers, CellTypeMarkers, and KnownMarkers classes here from pointillism.

Major changes:

• export: Reworked SingleCellExperiment method to support new BiocIO generic approach. This method functions similarly to SummarizedExperiment method, but also exports reducedDims matrices to disk as well.

Minor changes:

• Multiple changes to NAMESPACE, reflecting migration of code from pointillism.
• filterCells: Package metadata is now defined as "packageName" and "packageVersion", instead of previously using just "version".
• Migrated KnownMarkers generic from here to AcidGenerics. Previously this was defined in pointillism package.

AcidSingleCell 0.1.9 (2021-09-13)

Minor changes:

• Added aggregate method designed for SingleCellExperiment. Legacy method support for aggregateCols is still provided, but now works as a passthrough to aggregate, which is defined in AcidExperiment instead of here.
• Added assay support for filterCells and zerosVsDepth SingleCellExperiment methods.

AcidSingleCell 0.1.8 (2021-09-03)

Minor changes:

• Updated minimum dependencies and improved documentation.
• Improved code coverage, getting back to 100%.
• Improved CLI messages, using updated functions from AcidCLI.

AcidSingleCell 0.1.7 (2021-03-02)

Minor changes:

• Added logcounts and normcounts as reexports.

AcidSingleCell 0.1.6 (2021-02-26)

Minor changes:

• Renamed all instances of "blacklist" to "denylist".

AcidSingleCell 0.1.5 (2021-02-22)

Minor changes:

• Enforcing lower camel case in sampleData.

AcidSingleCell 0.1.4 (2021-02-12)

Minor changes:

• Reworked NAMESPACE to reduce the number of imported packages.
• Renamed package title in DESCRIPTION to better match AcidExperiment.

AcidSingleCell 0.1.3 (2021-02-09)

Minor changes:

• Added SingleCellExperiment-class to reexports.

AcidSingleCell 0.1.2 (2021-02-08)

Minor changes:

• Added SingleCellExperiment to reexports.

AcidSingleCell 0.1.1 (2021-02-08)

Minor changes:

• Improved code coverage, migrating unit tests from basejump.
• Improved package documentation.

AcidSingleCell 0.1.0 (2021-02-05)

Initial release, migrating code previously defined in basejump.

acidgenomics/r-acidsinglecell documentation built on March 30, 2024, 5:39 a.m.