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.

basejump 0.12.11 (2020-08-13)

Minor changes

  • Now reexporting requireNamespaces from AcidBase package.

basejump 0.12.12 (2020-08-18)

New methods

  • intersectAll: Defined list method.
  • intersectionMatrix: Defined list method.

basejump 0.12.13 (2020-08-25)

Minor changes

  • Migrated some globals to AcidBase package, for improved consistency.

basejump 0.12.14 (2020-09-14)

New functions

  • splitByLevel: Easily split a data frame into a list using a defined factor column (f argument). Can easily include the reference level with ref = TRUE, which is useful for statistical calculations on pairwise contrasts.

basejump 0.12.15 (2020-09-25)

New classes

  • Protein2Gene: DataFrame with proteinID, geneID, and geneName columns. Use corresponding makeProtein2GeneFromEnsembl to generate object simplify using Ensembl protein IDs as input.

New functions

  • getEnsDb: Now exporting function that was used internally to obtain EnsDb object from AnnotationHub.
  • makeProtein2GeneFromEnsembl: New utility function that takes Ensembl protein identifiers as input, and returns corresponding gene identifiers and gene names (i.e. HUGO gene symbols).

Minor changes

  • Reworked some internal code in makeGRangesFromEnesmbl to enable export of new getEnsDb function.
  • Reworked internal handling of AnnotationHub and EnsDb metadata.
  • makeGRangesFromEnsembl / getEnsDb: Improved sorting of Ensembl releases so that current release greater than 99 returns as expected. Since Ensembl is now at 101, we need to convert to integers internally instead of attempting to sort on strings.

basejump 0.12.16 (2020-09-29)

Minor changes

  • makeProtein2GeneFromEnsembl: Improved error message on match failure. Now returns the protein IDs that failed to match more clearly.

basejump 0.12.17 (2020-10-01)

Minor changes

  • makeSummarizedExperiment: No longer requiring primary assay defined to be named “counts”. This isn’t appropriate for SummarizedExperiment objects defined in the new DepMapAnalysis package.