NEWS.md

In acidgenomics/acidData: Acid Genomics Test Data

Release notes

AcidTest 0.9.0 (2023-11-08)

• Added DFrameList, GRangesList, and SplitDFrameList objects.

AcidTest 0.8.0 (2023-10-04)

• Resaved all example objects.

AcidTest 0.7.1 (2023-04-12)

• Resaved all example objects.

AcidTest 0.7.0 (2022-06-09)

• Migrated Seurat and SeuratMarkersPerCluster objects back here from pointillism, to avoid data NAMESPACE issues with rcmdcheck.

AcidTest 0.6.1 (2022-05-23)

• Resaved all example objects.

AcidTest 0.6.0 (2022-05-05)

• Now requiring R 4.2 / Bioconductor 3.15.
• Resaved all example objects.

AcidTest 0.5.0 (2022-03-10)

• Resaved all objects following Bioconductor 3.14 release.
• Renamed SingleCellExperiment to SingleCellExperiment_splatter.
• Migrated example Seurat object back to pointillism.

AcidTest 0.4.4 (2021-09-13)

• Resaved all objects.
• SummarizedExperiment and SummarizedExperiment_transcripts now contain metadata defined in rowData.

AcidTest 0.4.3 (2021-02-12)

• Resaved some objects: GRanges (now an expected unclassed EnsemblGenes), RangedSummarizedExperiment, Seurat, SingleCellExperiment, SingleCellExperiment_Seurat, and SingleCellExperiment_lanesplit.

AcidTest 0.4.2 (2021-02-05)

New data:

• Saved SingleCellExperiment_lanesplit example object.

Minor changes:

• Resaved objects, including transcript versions where applicable.

AcidTest 0.4.1 (2021-01-14)

Minor changes:

• Resaved metadata in strict lower camel case, where applicable.

AcidTest 0.4.0 (2020-10-06)

Major changes:

• Renamed package from acidtest to AcidTest.

acidtest 0.3.2 (2020-07-24)

• Resaved Seurat object.

acidtest 0.3.1 (2020-07-23)

Minor changes:

• Maintenance release, increasing R dependency to 4.0.

acidtest 0.3.0 (2020-03-16)

• Resaved all example datasets.
• Now using Ensembl 99 as reference instead of 92, where applicable. This helps avoid errors in other packages, namely pfgsea due to current Ensembl server migration (until March 24th) that renders all archives inaccessible, causing biomaRt code to error out.

acidtest 0.2.14 (2020-01-28)

• Additional documentation fixes to avoid CRAN warnings related to roxygen2 not outputting correct usage example for data when lazyData: FALSE.

acidtest 0.2.13 (2020-01-28)

• Documentation fixes to pass CRAN release checks.

acidtest 0.2.12 (2020-01-27)

• Removed monocle3 cell_data_set example object. Will add back when monocle3 is available on Bioconductor.

acidtest 0.2.11 (2020-01-20)

• Reverted saved version of SingleCellExperiment back to v0.2.8 version, as too many unit tests will fail in basejump otherwise, due to splatter creating a new random count matrix.

acidtest 0.2.10 (2020-01-19)

• Migrated band_instruments and band_members (dplyr join examples) from now archived transformer package here to acidtest.

acidtest 0.2.9 (2020-01-18)

• Renamed DataFrame example to DFrame, based on Bioconductor 3.10 change.
• Resaved all example objects.

acidtest 0.2.8 (2019-11-11)

• Resaved cell_data_set object.

acidtest 0.2.7 (2019-10-30)

• Resaved objects following Bioconductor 3.10 release.

acidtest 0.2.6 (2019-10-21)

• No longer checking against NA for syntactic functions.

acidtest 0.2.5 (2019-08-27)

• Updated R dependency to 3.6.

acidtest 0.2.4 (2019-08-13)

• Resaved Seurat and SingleCellExperiment_Seurat objects.
• Added additional comments regarding how to configure reticulate and UMAP to generate an example Seurat object with dimension reduction applied.

acidtest 0.2.3 (2019-08-10)

• SingleCellExperiment: Updated example to zero pad both row and column names. Previously, only the column names were padded.
• Improved reticulate documentation on how to process Seurat.

acidtest 0.2.2 (2019-08-02)

• cell_data_set: New example monocle3 cell_data_set S4 object.

acidtest 0.2.1 (2019-07-30)

• RangedSummarizedExperiment: Resaved with additional metadata columns in rowData that are useful for unit testing in DESeqAnalysis package.

acidtest 0.2.0 (2019-07-21)

• Disabled lazy data loading.
• Spelled out object class names to make example data more straightforward.
• Saved additional SingleCellExperiment and SummarizedExperiment examples.
• There's no currently no supported way to redirect old data names, so these changes are breaking.

acidtest 0.1.5 (2019-07-16)

• Added seurat example, migrated from pointillism package.
• Resaved sce based on new seurat object.
• Archived source code for previous sce as sce_splatter.R.

acidtest 0.1.4 (2019-07-12)

• Added dt example data.table object.
• Improved documentation consistency.

acidtest 0.1.3 (2019-07-11)

• Added ir example IRanges object.

acidtest 0.1.2 (2019-05-05)

• Now pinned to R >= 3.5.

acidtest 0.1.1 (2019-04-01)

• Added gr, lfc, mn, and txse test data.

acidtest 0.1.0 (2019-03-28)

• Initial release.

acidgenomics/acidData documentation built on Nov. 9, 2023, 6:01 a.m.