camelCase
on character vectors, instead
of attempting to directly sanitize GRanges
or DataFrame
class objects.
The Bioconductor S4 methods capable of these approaches have been moved from
syntactic to basejump.makeGRangesFromGFF
: Added ignoreTxVersion
argument, similar to tximport
convention, which allows the user to rename the transcriptID
column to
include the transcript version (e.g. ENST00000000233.10). This is useful for
matching identifiers in kallisto output processed directly from an Ensembl
FASTA reference transcriptome.Updated R dependency to 3.6.
makeGRangesFromEnsembl
: Bug fix for recent ensembldb update that added
AH73986
(Ensembl 79), which appears to be newer than AH73881
(Ensembl 97)
when sorting by AnnotationHub identifier. We've hardened the internal code
to instead sort by title, which resolves this issue.Bumped version to reflect change in basejump dependencies.
ensemblReleaseArchive
data, which maps the Ensembl release to the
Ensembl archive host URL.makeGRangesFromEnsembl
: Detect organisms with complex names including 3
words (e.g. Canis lupus familiaris) and automatically sanitize to the 2
word convention used internally by ensembldb (e.g. Canis familiaris). Thanks
@umasaxena for the heads up on this.emptyRanges
: Renamed mcolsNames
to mcolnames
, for better consistency
with the basejump naming conventions. Note that this formal is currently used
by basejump and bcbioSingleCell.data-raw/
scripts used to general minimal GFF example files..makeGenesFromEnsemblGTF
and .makeTranscriptsFromEnsemblGTF
: Made assert
checks less strict. No longer requiring gene_biotype
or gene_name
, so we
can pass through GRanges generated from FlyBase or WormBase.organism_mappings
data to organismMappings
, to improve camel
case consistency in package.Initial release. Migrated Ensembl AnnotationHub and GFF/GTF parsing functions here from the basejump package.
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