Providing tools for microRNA (miRNA) text mining. miRetrieve summarizes miRNA literature by extracting, counting, and analyzing miRNA names, thus aiming at gaining biological insights into a large amount of text within a short period of time. To do so, miRetrieve uses regular expressions to extract miRNAs and tokenization to identify meaningful miRNA associations. In addition, miRetrieve uses the latest miRTarBase version 8.0 (Hsi-Yuan Huang et al. (2020) "miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database" <doi:10.1093/nar/gkz896>) to display field-specific miRNA-mRNA interactions. The most important functions are available as a Shiny web application under <https://miretrieve.shinyapps.io/miRetrieve/>.
| Version: | 1.3.4 |
| Depends: | R (≥ 3.1.0) |
| Imports: | dplyr (≥ 1.0.7), forcats (≥ 0.5.1), ggplot2 (≥ 3.3.5), magrittr (≥ 2.0.1), openxlsx (≥ 4.2.4), plotly (≥ 4.9.4.1), purrr (≥ 0.3.4), readr (≥ 2.0.1), readxl (≥ 1.3.1), rlang (≥ 0.4.11), scales (≥ 1.1.1), stringr (≥ 1.4.0), textclean (≥ 0.9.3), tidyr (≥ 1.1.3), tidytext (≥ 0.3.1), topicmodels (≥ 0.2.12), wordcloud (≥ 2.6), xml2 (≥ 1.3.2), zoo (≥ 1.8-9) |
| Suggests: | kableExtra, knitr, reshape2, rmarkdown, testthat |
| Published: | 2021-09-18 |
| DOI: | 10.32614/CRAN.package.miRetrieve |
| Author: | Julian Friedrich [aut, cre], Hans-Peter Hammes [aut], Guido Krenning [aut] |
| Maintainer: | Julian Friedrich <julian.friedrich at medma.uni-heidelberg.de> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Materials: | README NEWS |
| CRAN checks: | miRetrieve results |
| Reference manual: | miRetrieve.pdf |
| Package source: | miRetrieve_1.3.4.tar.gz |
| Windows binaries: | r-devel: miRetrieve_1.3.4.zip, r-release: miRetrieve_1.3.4.zip, r-oldrel: miRetrieve_1.3.4.zip |
| macOS binaries: | r-release (arm64): miRetrieve_1.3.4.tgz, r-oldrel (arm64): miRetrieve_1.3.4.tgz, r-release (x86_64): miRetrieve_1.3.4.tgz, r-oldrel (x86_64): miRetrieve_1.3.4.tgz |
| Old sources: | miRetrieve archive |
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