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Fixed a bug that prevented miRetrieve from loading MEDLINE-files
after the dependency readr was updated.
Added a device argument in save_plot(),
based on ggplot’s ggsave() function.
Converts non-ASCII characters to ASCII characters when extracting
miRNAs. miRetrieve now converts non-ASCII characters in text to ASCII
characters using the textclean package. By doing so,
miRetrieve is able to summarize miRNAs with apparently the same, but on
a bit-code level different spelling, thereby increasing extraction
efficacy.
Added a miRetrieve website. The package now comes with an own
website, hosted on GitHub under
https://julfriedrich.github.io/miRetrieve/, courtesy to
pkgdown.
Added miRTarBase 8.0 to miRetrieve. miRTarBase 8.0 can now be
queried with miRetrieve using join_mirtarbase(). If you use
miRetrieve to visualize miRNA-mRNA interactions based on miRTarBase,
please make sure to cite Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li,
et al., miRTarBase 2020: updates to the experimentally validated
microRNA–target interaction database, Nucleic Acids Research, Volume 48,
Issue D1, 08 January 2020, Pages D148–D154,
https://doi.org/10.1093/nar/gkz896.
Converts miRNA names of older miRBase versions to the newest miRBase version 22 when extracted (e.g. miR-97, miR-102, miR-180(a/b) become miR-30a, miR-29a, and miR-172(a/b))
Renamed read_pubmed_xml() to
read_pubmed_jats()
Added unit tests
read_pubmed() to adapt the function to
the newest R versionWelcome to miRetrieve! miRetrieve is designed for microRNA text mining in abstracts. By extracting, counting, and analyzing miRNA names from literature, miRetrieve aims at providing biological insights from a large amount of text within a short period of time.
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.