miRetrieve: miRNA Text Mining in Abstracts

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 (≥, 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
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_1.3.2.tgz, r-release (x86_64): miRetrieve_1.3.4.tgz, r-oldrel: miRetrieve_1.3.4.tgz
Old sources: miRetrieve archive


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