The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

bedr 1.1.3 (2025-04-04)

Added

• Add method argument to in.region function

Changed

• Update changelog to Markdown NEWS.md format
• Use updated renv GitHub action for R CMD check
• Rename internal helper function parse.vcf.header() to prep.vcf.header() to avoid naming conflict with base R parse() S3 method.

Fixed

• Replace outdated autostart in fread with skip.
• Fix cross-reference format in manual
• Update GitHub links

bedr 1.1.2 (2024-01-24)

Added

• Add LICENSE.md to repository
• Update DESCRIPTION to include URL and BugReports links

bedr 1.1.1 (2023-08-24)

Changed

• Update CI/CD action

Removed

• Remove unnecessary package manual file

bedr 1.1.0 (2022-03-01)

Added

• Add vcf2bedpe module to convert structural variant calls obtained from Manta, GRIDSS and Delly v0.7.8

bedr 1.0.7 (2019-04-01)

Changed

• forced vcf2bed not to print genomic coordinates in R scientific notation for interoperability with other processors

bedr 1.0.6 (2019-01-12)

Fixed

• Updated support for tabix version >1.1. tabix deprecated option -B is now replaced with -R

bedr 1.0.5

Fixed

• fixed incorrect ordering of chromosome table returned by get.chr.length() - [rolled back]

bedr 1.0.4 (2017-10-12)

Changed

• Added rmarkdown in Suggests section
• Parameterised test.region.similarity() with gaps.file and repeats.file to support custom files
• Exposed utility function bed2index() via NAMESPACE to support its direct usage

Fixed

• Fixed bug when bedtools ‘coverage’ output is post-processed in bedr
• Fixed is.valid.seq() to comply with inputs and outputs as described in docs

bedr 1.0.3 (2016-08-23)

Changed

• Standardised function name; renamed snm() to bedr.snm.region()
• Listed SystemRequirements to the package metadata
• Added support for Human hg38 genome assembly

bedr 1.0.2 (2015-09-21)

Fixed

• Fixed compatibility with data.table >= v1.9.6 for data.table::fread() call

bedr 1.0.1 (2015-09-05)

Fixed

• Fixed sort –version command as Solaris does not support –version which is GNU specific

bedr 1.0.0 (2015-09-03)

Added

• Initial release

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.
Health stats visible at Monitor.