NEWS

---

ensembldb 2.29.1

• Improve documentation of 'proteinToGenome()' and require named 'IRanges' as input to 'proteinToGenome()'.

ensembldb 2.27.1

• Functions for coordinate mapping gain support for pre-loaded genomic ranges hence enabling parallel processing support (contribution from Boyu Yu).

ensembldb 2.25.1

• Skip reading gtf file from Ensembl ftp server in unit test.

ensembldb 2.23.2

• Fix SQLite database names to include also the subspecies.

ensembldb 2.23.1

• Remove disjointExons method.

ensembldb 2.21.5

• Fix spell mistakes (thanks to Mike Love).

ensembldb 2.21.3

• Add minimal required Ensembl API version for certain data fields (stable_id_version). Issue https://github.com/jorainer/ensembldb/issues/139

ensembldb 2.21.1

• Since *is circular* flag for chromosomes extracted using the Ensembl Perl API is always 'FALSE': manually set 'isCircular' to 'TRUE' for chromosome(s) named '"MT"' (issue https://github.com/jorainer/ensembldb/issues/133).

ensembldb 2.19.10

• Fix issue in 'getGeneRegionTrackForGviz' if no transcript was found in the provided genomic range (issue https://github.com/jorainer/ensembldb/issues/132).

ensembldb 2.19.9

• 'seqlevelsStyle' allows to provide a custom mapping data frame.

ensembldb 2.19.8

• Require package Biostrings in the coordinate mapping vignette.

ensembldb 2.19.7

• 'listColumns' does no longer report columns from the metadata database table (issue https://github.com/jorainer/ensembldb/issues/128).

ensembldb 2.19.6

• Fixes in 'proteinToGenome'.

ensembldb 2.19.5

• Add support for additional 'tx_is_canonical' column and add 'TxIsCanonicalFilter' (issue https://github.com/jorainer/ensembldb/issues/123).

ensembldb 2.19.4

• Fix issue with quotes in transcript names when importing transcript tables.

ensembldb 2.19.2

• Restore backward compatibility (issue https://github.com/jorainer/ensembldb/issues/122).

ensembldb 2.19.1

• Add database column tx_name to store the external transcript names.
• Update TxNameFilter to allow filtering on this database column.

ensembldb 2.17.4

• Fix issue with extracting 5' or 3' UTRs for transcript without UTRs.

ensembldb 2.17.3

• Make parameter 'port' optional in the script to create EnsDb databases.

ensembldb 2.17.2

• Disable ideogram plotting in vignettes.

ensembldb 2.17.1

• Fix error when importing uncompressed GTF files.

ensembldb 2.15.3

• Fix missing declaration of rmarkdown.

ensembldb 2.15.2

• Ensure remote gzipped files are handled properly by 'ensDbFromGtf'.

ensembldb 2.15.1

• Add new field canonical_transcript to the gene table reporting the ID of the gene's canonical transcript.

ensembldb 2.11.1

• Fix mapIds issue.
• Add gc_count to the transcripts table.
• Ensure 'mapIds' returns a result equal to the number of input keys - even if none of them could be mapped (issue #104).

ensembldb 2.7.10

• Export getGenomeTwoBitFile (issue #95).
• Update vignette on using getGenomeTwoBitFile instead of getGenomeFaFile.

ensembldb 2.7.9

• Add intronsByTranscript method (issue #94).

ensembldb 2.7.7

• Performance improvement for proteinToTranscript.

ensembldb 2.7.6

• Increase performance of genomeToTranscript for input GRanges of length > 1.

ensembldb 2.7.5

• Fix class definitions for R >= 3.6.

ensembldb 2.7.4

• Update perl script to add columns tx_id_version and gene_id_version to the transcript and gene database tables.

ensembldb 2.7.3

• Implement mapIds multiVals = "CharacterList" option (issue #87).

ensembldb 2.7.2

• Add vignette with coordinate mapping use cases

ensembldb 2.7.1

• transcriptToGenome returns an empty GRanges if the input range is outside of the transcript's sequence instead of throwing an error.

ensembldb 2.5.9

• Write the official scientific name into the "Organism" metadata field.

ensembldb 2.5.8

• Further improve MySQL support and performance.

ensembldb 2.5.6

• Add additional (integer) ID columns to the tables for the MySQL backend to improve performance.
• Use integer primary key columns for join queries in MySQL/MariaDB EnsDb databases.

ensembldb 2.5.5

• Switch from RMySQL to RMariaDB.

ensembldb 2.5.2

• Switch from GenenameFilter to GeneNameFilter for AnnotationHub >= 1.5.2.

ensembldb 2.5.1

• Fix bug in getGeneRegionTrackForGviz that throws an error if both protein coding and non-coding transcripts are fetched.

ensembldb 2.3.14

• New ProteinDomainSourceFilter and ProteinDomainIdFilter.

ensembldb 2.3.11

• Fix for issue #75.

ensembldb 2.3.9

• Add transcriptToCds and cdsToTranscript functions (issue #73).

ensembldb 2.3.8

• Fix problem creating EnsDb from GTF file lacking exon IDs (issue #72, https://support.bioconductor.org/p/105536/).

ensembldb 2.3.7

• Switch to EnsDb.Hsapiens.v86 in examples, unit tests and vignettes.

ensembldb 2.3.6

• Fix issue #69 failing to map genomic coordinates to proteins if different genomic coordinates are mapped to the same transcripts/proteins.

ensembldb 2.3.5

• Fix problem mapping genomic coordinates on named GRanges.

ensembldb 2.3.2

• Functionality to between genomic and transcript-relative or protein-relative coordinates: proteinToTranscript, genomeToTranscript, transcriptToGenome, transcriptToProtein, genomeToProtein.

ensembldb 2.3.1

• Functionality to map within-protein coordinates to genomic coordinates: proteinToGenome function.

ensembldb 2.1.12

• Use new defaults from the IRanges package for arguments maxgap = -1L, minoverlap = 0L in transcriptsByOverlaps and exonsByOverlaps methods.
• Remove RSQLite warnings (issue #54).

ensembldb 2.1.11

• ensDbFromGtf failed to parse header for GTF files with more than one white space.

ensembldb 2.1.10

• supportedFilters returns a data frame with the filter class name and corresponding field (column) name.

ensembldb 2.1.9

• Support for global filters in an EnsDb object.
• Add filter function.

ensembldb 2.1.8

• New annotations available in EnsDb objects: gene.description and tx.tx_support_level.
• New TxSupportLevelFilter object.

ensembldb 1.99.13

• Most filter classes are now imported from the AnnotationFilter package.
• Parameter 'filter' supports now filter expression.
• Multiple filters can be combined with & and |.
• buildQuery is no longer exported.

ensembldb 1.99.11

• ensDbFromGtf failed to fetch sequence length for some ensemblgenomes versions.
• Retrieving also the taxonomy ID from the Ensembl databases and storing this information into the metadata table.

ensembldb 1.99.10

• Fix problem on Windows systems failing to download files from Ensembl servers.

ensembldb 1.99.6

• MySQL database name for useMySQL was not created as expected for GTF/GFF based EnsDbs.

ensembldb 1.99.5

• OnlyCodingTxFilter is now exported. This filter allows to query for protein coding genes.

ensembldb 1.99.3

• Add two additional uniprot table columns to internal variable and fix failing unit test.
• Add two additional uniprot table columns to internal variable and fix failing unit test.
• UniprotdbFilter and UniprotmappingtypeFilter.
• Fetching Uniprot database and the type of mapping method for Uniprot IDs to Ensembl protein IDs: database columns uniprot_db and uniprot_mapping_type.

ensembldb 1.99.2

• Perl script is no longer failing if no chromosome info is available.

ensembldb 1.99.1

• No protein table indices were created when inserting an EnsDb with protein data to MySQL.

ensembldb 1.99.0

• The perl script to create EnsDb databases fetches also protein annotations.
• Added functionality to extract protein annotations from the database (if available) ensuring backward compatibility.
• Add proteins vignette.
• Improved functionality to fetch sequence lengths for chromosomes from Ensembl or ensemblgenomes.

ensembldb 1.5.14

• listEnsDbs function to list EnsDb databases in a MySQL server.
• EnsDb constructor function allows to directly connect to a EnsDb database in a MySQL server.
• useMySQL compares the creation date between database and SQLite version and proposes to update database if different.

ensembldb 1.5.13

• useMySQL method to insert the data into a MySQL database and switch backend from SQLite to MySQL.

ensembldb 1.5.12

• Add additional indices on newly created database which improves performance considerably.
• Fix issue #11: performance problems with RSQLite 1.0.9011. Ordering for cdsBy, transcriptsBy, UTRs by is performed in R and not in SQL.
• Fix ordering bug: results were sorted by columns in alphabetical order (e.g. if order.by = "seq_name, gene_seq_start" was provided they were sorted by gene_seq_start and then by seq_name

ensembldb 1.5.11

• makeEnsemblSQLiteFromTables and ensDbFromGRanges perform sanity checks on the input tables.

ensembldb 1.5.10

• Using html_document2 style for the vignette.

ensembldb 1.5.9

• New SymbolFilter.
• returnFilterColumns method to enable/disable that filter columns are also returned by the methods (which is the default).
• select method support for SYMBOL keys, columns and filter.
• Select method does ensure result ordering matches the input keys if a single filter or only keys are provided.

ensembldb 1.5.8

• Fix problem with white space separated species name in ensDbFromGRanges.

ensembldb 1.5.7

• Fixed typos in documentation

ensembldb 1.5.6

• Fix warning fo validation of numeric BasicFilter.

ensembldb 1.5.5

• exonsBy: did always return tx_id, even if not present in columns argument.

ensembldb 1.5.4

• Column tx_id was always removed from exonsBy result even if in the columns argument.
• exon_idx was of type character if database generated from a GTF file.

ensembldb 1.5.2

• tx_id was removed from metadata columns in txBy.
• Fixed a bug that caused exon_idx column to be character if database created from a GTF.

ensembldb 1.5.1

• Added support for column tx_name in all methods and in the keys and select methods. Values in the returned tx_name columns correspond to the tx_id.
• Update documentation.

ensembldb 1.3.20

• methods transcripts, genes etc don't result in an error when columns are specified which are not present in the database and the return.type is GRanges.
• Removed the transcriptLengths method implemented in ensembldb in favor of using the one from GenomicFeatures.

ensembldb 1.3.19

• ensDbFromGRanges (and thus ensDbFromGtf, ensDbFromGff and ensDbFromAH) support now Ensembl GTF file formats from version 74 and before.

ensembldb 1.3.18

• New ExonrankFilter to filter based on exon index/rank.

ensembldb 1.3.17

• Use setdiff/intersect instead of psetdiff/pintersect.

ensembldb 1.3.16

• Fixed failing test.

ensembldb 1.3.15

• GRangesFilter now supports GRanges of length > 1.
• seqlevels method for GRangesFilter.
• New methods exonsByOverlaps and transcriptsByOverlaps.

ensembldb 1.3.14

• seqlevelsStyle getter and setter method to change the enable easier integration of EnsDb objects with UCSC based packages. supportedSeqlevelsStyle method to list possible values. Global option "ensembldb.seqnameNotFound" allows to adapt the behaviour of the mapping functions when a seqname can not be mapped properly.
• Added a seqlevels method for EnsDb objects.
• Add an example to extract transcript sequences directly from an EnsDb object to the vignette.
• Add examples to use EnsDb objects with UCSC chromosome names to the vignette.
• Seqinfo for genes, transcripts and exons contain now only the seqnames returned in the GRanges, not all that are in the database.

ensembldb 1.3.13

• EnsDb: new "hidden" slot to store additional properties and a method updateEnsDb to update objects to the new implementation.
• New method "transcriptLengths" for EnsDb that creates a similar data.frame than the same named function in the GenomicFeatures package.
• fiveUTRsByTranscript and threeUTRsByTranscript returned wrong UTRs for some special cases in which the CDS start and end were in the same exon. This has been fixed.

ensembldb 1.3.12

• ensDbFromGff and ensDbFromAH functions to build EnsDb objects from GFF3 files or directly from AnnotationHub ressources.
• getGenomeFaFile does now also retrieve Fasta files for the "closest" Ensembl release if none is available for the matching version.
• Removed argument 'verbose' in ensDbFromGRanges and ensDbFromGtf.
• Updated parts of the vignette.
• Removed method extractTranscriptSeqs again due to some compatibility problems with GenomicRanges.
• Avoid wrong CDS start/end position definition for Ensembl gtf files in which the start or end codon is outside the CDS.

ensembldb 1.3.11

• "select" method returns now also the keytype as a column from the database.

ensembldb 1.3.10

• Implemented methods columns, keys, keytypes, mapIds and select from AnnotationDbi.
• Methods condition<- and value<- for BasicFilter.

ensembldb 1.3.9

• The shiny app now allows to return the search results.

ensembldb 1.3.7

• Some small changes to the vignette.
• Fixed a problem in an unit test.

ensembldb 1.3.6

• Fixed a bug in ensDbFromGRanges.

ensembldb 1.3.5

• Added GRangesFilter enabling filtering using a (single!) GRanges object.
• Better usability and compatibility with chromosome names: SeqnameFilter and GRangesFilter support both Ensembl and UCSC chromosome names, if option ucscChromosomeNames is set to TRUE returned chromosome/seqnames are in UCSC format.
• Added method "value" for BasicFilter objects.
• transcripts, genes, exons return now results sorted by seq name and start coordinate.

ensembldb 1.3.4

• Added extractTranscriptSeqs method for EnsDb objects.
• Added a section to the vignette describing the use of ensembldb in Gviz.
• Fixed the vignette to conform the "Bioconductor style".
• Added argument use.names to exonsBy.
• Fixed bug with getGeneRegionTrackForGviz with only chromosome specified.
• Fixed an internal problem subsetting a seqinfo.

ensembldb 1.3.3

• Add method getGeneRegionTrackForGviz to enable using EnsDb databases for Gviz.
• cdsBy, fiveUTRsForTranscript and threeUTRsForTranscript do no longer throw an error if nothing was found but return NULL and produce a warning.

ensembldb 1.3.2

• Implemented methods cdsBy, fiveUTRsForTranscript and threeUTRsForTranscript for EnsDb.

ensembldb 1.3.1

• Ensuring that methods exons, genes and transcripts return columns in the same order than provided with argument 'columns' for return.type 'data.frame' or 'DataFrame'.

ensembldb 1.1.9

• Fixed a figure placement problem that can result in an error on certain systems using a recent TexLive distribution.

ensembldb 1.1.6

• Fix a bug in lengthOf that caused an error if no filter was supplied.

ensembldb 1.1.5

• Implemented a shiny web app to search for genes/transcripts/exons using annotation of an EnsDb annotation package (function runEnsDbApp).

ensembldb 1.1.4

• Added promoters method.

ensembldb 1.1.3

• Added method ensemblVersion that returns the Ensembl version the package bases on.
• Added method getGenomeFaFile that queries AnnotationHub to retrieve the Genome FaFile matching the Ensembl version of the EnsDb object.

ensembldb 1.1.2

• Added examples to the vignette for building an EnsDb using AnnotationHub along with the matching genomic sequence.
• Added an example for fetching the sequences of genes, transcripts and exons to the vignette.
• Fixed a bug in ensDbFromGRanges and ensDbFromGtf in which the genome build version was not set even if provided.

ensembldb 1.1.1

• The filter argument in all functions supports now also submission of a filter object, not only of a list of filter objects.

ensembldb 0.99.18

• Fixed a problem in processing GTF files without header information.
• Fixed a bug failing to throw an error if not all required feature types are available in the GTF.

ensembldb 0.99.17

• Added new function ensDbFromGRanges that builds an EnsDB database from information provided in a GRanges object (e.g. retrieved from the AnnotationHub).

ensembldb 0.99.16

• Added argument outfile to ensDbFromGtf that allows to manually specify the file name of the database file.
• ensDbFromGtf tries now to automatically fetch the sequence lengths from Ensembl.
• Fixed the function that extracts the genome build version from the gtf file name.

ensembldb 0.99.15

• metadata method to extract the information from the metadata database table.
• ensDbFromGtf function to generate a EnsDb SQLite file from an (Ensembl) GTF file.

ensembldb 0.99.14

• Fixed a problem when reading tables fetched from Ensembl that contained ' or #.

ensembldb 0.99.13

• Added argument "port" to the fetchTablesFromEnsembl to allow specifying the MySQL port of the database.

ensembldb 0.99.12

• argument "x" for method organism changed to "object".