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biomartr 1.0.7

New features

Generalization of Biomart database access #108

Bug fixes

biomartr 1.0.6

New features

Bug fixes

biomartr 1.0.5

Package generalization

Over 5000 lines have been edited, most of them removed (#100), to generalize the package to make it more safe for future development. This progress is still ongoing.

New features

Power user cache

The package now supports caching of back end files which used to be saved to /tmp folder (i.e. lost on computer restart). This make it easy for power users who want higher speed. For more info, see the function ?cachedir_set

Bug fixes

biomartr 1.0.4

New Features

Bug Fixes

biomartr 1.0.3

biomartr 1.0.2

New Functions

Example:

# define scientific names of species for which
# collections shall be retrieved
organism_list <- c("Arabidopsis thaliana", 
                   "Arabidopsis lyrata", 
                   "Capsella rubella")
# download the collection of Arabidopsis thaliana from refseq
# and store the corresponding genome file in '_ncbi_downloads/collection'
 getCollectionSet( db       = "refseq", 
             organism = organism_list, 
             path = "set_collections")

New Features

Ath_path <- biomartr::getGFF(organism = "Arabidopsis thaliana", remove_annotation_outliers = TRUE)

Bug Fixes

biomartr 0.9.2 - minor changes to comply with CRAN policy regarding Internet access failure -> Instead of using warnings or error messages, only gentle messages are allowed to be used

biomartr 0.9.0

Please be aware that as of April 2019, ENSEMBLGENOMES was retired (see details here). Hence, all biomartr functions were updated and won’t support data retrieval from ENSEMBLGENOMES servers anymore.

New Functions

New Features of Existing Functions

biomartr 0.8.0

New Functions

New Functionality of Existing Functions

biomartr 0.7.0

Function changes

New Functions

biomartr 0.5.2

Bug fixes

biomartr 0.5.1

Bug fixes

New Functions

Function changes

biomartr 0.4.0

Bug fixes

New Functions

Function changes

Vignette updates

biomartr 0.3.0

Bug fixes

biomartr 0.2.1

In this version of biomartr the organism*() functions were adapted to the new ENSEMBL 87 release in which organism name specification in the Biomart description column was changed from a scientific name convention to a mix of common name and scientific name convention.

biomartr 0.2.0

In this version, biomartr was extended to now retrieve genome, proteome, CDS, GFF and meta-genome data also from ENSEMBL and ENSEMLGENOMES. Furthermore, all NCBI retrieval functions were updated to the new server folder structure standards of NCBI.

New Functions

Function changes

Vignette updates

biomartr 0.1.0

biomartr 0.0.3

Vignettes

biomartr 0.0.2

Vignettes

biomartr 0.0.1

Release Version

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.