basejump 0.12.0 (2020-01-20)

Major changes

  • Migrated functions from brio (now renamed to pipette), freerange, and transformer, in preparation for Bioconductor submission and reviews.
  • Updated messages to utilize the cli package.

basejump 0.12.1 (2020-01-30)

Major changes

  • Reworked aggregate, aggregateCols, aggregateRows support to reflect internal migration away from Matrix.utils dependency.

Minor changes

  • NAMESPACE fix for unexpected removal of Matrix.utils from CRAN. Now defining the previously imported aggregate.Matrix function directly here in basejump.
  • aggregate: Now defining matrix method.
  • aggregate* generics now consistently use “x” instead of “object”.

basejump 0.12.2 (2020-02-18)

Minor changes

  • Migrating pseudobulk methods to pointillism package. Rethinking the approach used here to work better with per-cluster aggregation operations. Will be updated in the next pointillism release.

basejump 0.12.3 (2020-02-24)

Minor changes

  • makeSingleCellExperiment, makeSummarizedExperiment: Removed spikeNames support due to a breaking change in SingleCellExperiment, which has removed isSpike in favor of altExps. Refer to the SingleCellExperiment documentation for updated current best practice for handling spike-in transcripts, which now requires slotting a separate SummarizedExperiment object containing things like ERCCs inside the main SingleCellExperiment.

basejump 0.12.4 (2020-03-15)

Minor changes

  • matchEnsemblReleaseToURL, matchHumanOrthologs: update unit tests to reflect Ensembl server migration, which has rendered Ensembl archives inaccessible via biomaRt until March 24th. Unit tests now check against current release instead of a pinned archive release.

basejump 0.12.5 (2020-05-11)

Minor changes

  • importSampleData: The pipeline = "cpi" option is now defunct. Use pipeline = "none', sheet = 2L for CPI samples.
  • importSampleData: Added optional autopadZeros argument for easy handling of sample identifiers, which are often input by users without correct padding. This helps easily convert sample_1, sample_2, … sample_10 to expected sample_01, sample_02, … sample_10 sorting. Currently disabled by default.
  • importTx2Gene: Added ignoreGeneVersion option, now enabled by default. This helps process gene identifiers by default in a manner suitable for downstream tximport-DESeq2 workflow.
  • headtail: Removed Unicode support in favor of simple ASCII return, to avoid build warnings in latest R 4.0 release version.
  • Miscellaneous unit test updates to reflect changes in DataFrame class and NCBI server updates.
  • camelCase, dottedCase, organism, snakeCase, upperCamelCase: S4 methods for DataFrame are now defined directly against DataFrame, instead of attempting to inherit from DataTable virtual class. This will break otherwise on bioc-devel 3.12, which seems to have changed inheritance.

basejump 0.12.6 (2020-05-17)

Minor changes

  • convertGenesToSymbols: Added method support for GRanges class objects. Automatically sets names as unique gene symbols.
  • HGNC2Ensembl: Enforce TSV handling internally in import call.
  • MGI2Ensembl: Fix for column name handling.

basejump 0.12.7 (2020-05-22)

Minor changes

  • aggregate, aggregateCols, aggregateRows: Relaxed assert checks on validity of dimnames, so we can use internally in acidgsea package, which needs to handle gene symbols containing syntactically invalid hyphens.

basejump 0.12.8 (2020-06-15)

Minor changes

  • autopadZeros: Migrated character method support to syntactic package, since this is useful for low-level code run inside koopa.

basejump 0.12.9 (2020-07-24)

Minor changes

  • Maintenance release, updating minimum R dependency to 4.0.

basejump 0.12.10 (2020-08-04)

Minor changes

  • Migrated alphaThreshold and lfcThreshold methods to DESeqAnalysis package. These are not used in other packages and may not be generally applicable to SummarizedExperiment class, so rethinking here.