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 (≥ 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 |
Documentation:
Downloads:
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