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.