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Version 0.2

AcidGenomes 0.2.0 (2021-02-02)

New functions:

  • Added new genome download functions, migrated from previous Python approach defined in py-koopa package.
  • Switched from cli to AcidCLI for interactive messages.

Major changes:

  • In metadata columns, renamed “ID” to “Id”, for stricter lower camel case formatting.
  • Now ensuring GenomicRanges gets attached as a dependency.
  • Now using BiocFileCache (via pipette::cacheURL internally) to automatically cache GFF/GTF files when used in makeGRangesFromGFF.
  • Renamed ignoreTxVersion to simply ignoreVersion, where applicable. We want this setting to also apply at gene level.
  • GFF, TxDb, and ensembldb parser functions now default to ignoreVersion = FALSE. Previous releases of AcidGenomes and basejump had this set to ignoreVersion = TRUE by default. Note that both modes are now non-destructive.
  • GRanges mcols now return with tx prefix instead of transcript.
  • GRanges mcols now use strict camel case formatting (e.g. geneId instead of geneID).

AcidGenomes 0.2.1 (2021-02-08)

Minor changes:

  • Now including some reexports from GenomicRanges and IRanges.

AcidGenomes 0.2.2 (2021-02-09)

Minor changes:

  • Reduced the number of reexported functions.

AcidGenomes 0.2.3 (2021-02-10)

Minor changes:

  • Reverted back to using vroom as importer for HGNC and MGI2Ensembl.

AcidGenomes 0.2.4 (2021-02-13)

New functions:

  • EntrezGeneInfo: New utility for obtaining gene annotations from NCBI.

Major changes:

  • geneSynonyms: Reworked internal code, extending EntrezGeneInfo.

AcidGenomes 0.2.5 (2021-02-17)

Minor changes:

  • Genome downloader functions (e.g. downloadEnsemblGenome) now return relative symlinks instead of absolute paths.
  • Bug fix for mapHumanOrthologs internal join step. Now returns humanGeneId and humanGeneName columns instead of hgncId and hgncName columns, which technically were incorrect, since these map to Ensembl.

AcidGenomes 0.2.6 (2021-02-25)

Minor changes:

  • Updated basejump dependency versions.
  • EntrezGeneInfo: Improved column formatting.

AcidGenomes 0.2.7 (2021-02-26)

Minor changes:

  • makeGRangesFromGFF: Improved support and code coverage for handling of bcbio-nextgen ref-transcripts.gtf genome file.

AcidGenomes 0.2.8 (2021-03-02)

Minor changes:

  • Relaxed validity checks for EnsemblGenes and EnsemblTranscripts.

AcidGenomes 0.2.9 (2021-03-03)

Minor changes:

  • Gene2Symbol functions now preserve metadata, as expected. This was causing pointillism package to error, due to unwanted breaking change.
  • Tx2Gene: Improved consistency of metadata return, ensuring call and synonyms are not defined.
  • Renamed internal “acidGenomes” metadata key to “packageVersion”, for consistency with conventions used in other Acid Genomics packages.

AcidGenomes 0.2.10 (2021-03-15)

Minor changes:

  • mapHumanOrthologs: Hardened mouse-to-human matching.
  • makeGRangesFromEnsembl: No longer hard-coding minimum release version check at 87, in case older releases are ported to AnnotationHub in a future release.
  • Revert back to ignoreVersion = TRUE by default for genome annotation importers, as this is typically what users expect by default.

AcidGenomes 0.2.11 (2021-03-19)

Minor changes:

  • HGNC now returns columns with split values as CharacterList, instead of as character strings containing “|”.

AcidGenomes 0.2.12 (2021-04-27)

Major changes:

  • Removed some Bioconductor packages from imports: AnnotationDbi, AnnotationHub, GenomeInfoDb, and ensembldb. This helps reduce package loading time and avoid unwanted BiocManager messages from appearing at startup (due to loading of AnnotationHub). These are included as suggested packages, which should not be problematic, since they are frequently used.

AcidGenomes 0.2.13 (2021-05-18)

  • Internal fixes to provide compatibility for R 4.1 release.
  • Updated dependencies to support Bioconductor 3.13.

AcidGenomes 0.2.14 (2021-06-10)

Minor changes:

  • Gene2Symbol: Improve handling when gene identifiers are integer, such as is the case with NCBI Entrez gene identifiers.

AcidGenomes 0.2.15 (2021-07-27)

Minor changes:

  • Added support for new Mus musculus GRCm39 genome build. Updated internal code for mapUCSCBuildToEnsembl and downloadEnsemblGenome, in particular. Note that *_chr_patch_hapl_scaff GFF and GTF files are no longer available on the Egnyte FTP server for GRCm39 (only GRCm38 and GRCh38).

AcidGenomes 0.2.16 (2021-08-09)

Major changes:

  • Removed mapEnsemblBuildToUCSC and mapUCSCBuildToEnsembl functions. Also removed mapping support for UCSC genome build names (e.g. “hg38”) inside of makeGRangesFromEnsembl calls, since this is not technically the correct genome build name.
  • downloadEnsemblGenome, downloadGencodeGenome, etc. now support file caching by default with cache = TRUE argument.

Minor changes:

  • Improved genome download code coverage.
  • Split out stripGeneVersions and stripTranscriptVersions documentation into separate files.
  • Reorganized S4 method documentation to be alphabetical consistently.
  • export: Hardened Tx2Gene method to ensure that rownames are consistently removed prior to export. Noticed that this was an issue with UCSC genome build download.

AcidGenomes 0.2.17 (2021-08-11)

Major changes:

  • Gene2Symbol: Hardened internal identifier mapping code in switch call to support format argument. Improved unit testing for expected behavior of format argument. Fixed “1:1” mapping to split based on geneName column rather than geneId column.
  • Tx2Gene: Improved code coverge and cleaned up internal complete.cases handling.
  • All identifier mapping classes (e.g. Ensembl2Entrez, Gene2Symbol, Tx2Gene) now check for complete.cases in S4 validity methods.

Minor changes:

  • currentEnsemblVersion and mapHumanOrthologs working examples are now re-enabled, wrapped in a try call.

AcidGenomes 0.2.18 (2021-09-03)

Minor changes:

  • Improved CLI message formatting.
  • downloadRefSeqGenome, downloadUCSCGenome: Improved the genomeBuild documentation, with more specific examples.

AcidGenomes 0.2.19 (2021-09-13)

Minor changes:

  • getEnsDb / makeGRangesFromEnsembl: Quieted down package loading from Bioconductor when obtaining annotations for GRCh37 (EnsDb.Hsapiens.v75 release package).
  • Improved CLI messages to use S4 class when applicable.

AcidGenomes 0.2.20 (2022-01-08)

Minor changes:

  • Tx2Gene class check: disabling check that looks for identical transcript and gene identifiers. This check is not compatible with the Saccharomyces cerevisiae (sacCer3) reference genome. Thanks for pointing this out @amizeranschi.