Package: miRetrieve 1.3.4

Julian Friedrich

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/>.

Authors:Julian Friedrich [aut, cre], Hans-Peter Hammes [aut], Guido Krenning [aut]

miRetrieve_1.3.4.tar.gz
miRetrieve_1.3.4.tar.gz(r-4.5-noble)miRetrieve_1.3.4.tar.gz(r-4.4-noble)
miRetrieve_1.3.4.tgz(r-4.4-emscripten)miRetrieve_1.3.4.tgz(r-4.3-emscripten)
miRetrieve.pdf |miRetrieve.html✨
miRetrieve/json (API)
NEWS

# Install 'miRetrieve' in R:
install.packages('miRetrieve', repos = 'https://cloud.r-project.org')
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.70 score 213 downloads 65 exports 107 dependencies

Last updated 4 years agofrom:1abaa407f9. Checks:3 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 15 2025
R-4.5-linuxOKMar 15 2025
R-4.4-linuxOKMar 15 2025

Exports:add_col_topicanimal_keywordsassign_topicassign_topic_ldabiomarker_keywordscalculate_score_animalscalculate_score_biomarkercalculate_score_patientscalculate_score_topiccombine_dfcombine_mircombine_stopwordscompare_mir_countcompare_mir_count_log2compare_mir_count_uniquecompare_mir_termscompare_mir_terms_log2compare_mir_terms_scattercompare_mir_terms_uniquecount_mircount_mir_thresholdcount_snpcount_targetextract_mir_dfextract_mir_stringextract_snpfit_ldagenerate_stopwordsget_distinct_mir_dfget_distinct_mir_vecget_mirget_pmidget_shared_mir_dfget_shared_mir_vecget_snpindicate_mirindicate_termjoin_mirtarbasejoin_targetspatients_keywordsplot_lda_termplot_mir_countplot_mir_count_thresholdplot_mir_developmentplot_mir_newplot_mir_termsplot_perplexityplot_score_animalsplot_score_biomarkerplot_score_patientsplot_score_topicplot_target_countplot_target_mir_scatterplot_wordcloudread_pubmedread_pubmed_jatssave_excelsave_plotsubset_dfsubset_mirsubset_mir_thresholdsubset_researchsubset_reviewsubset_snpsubset_year

Dependencies:askpassbase64encBHbitbit64bslibcachemcellrangerclicliprcolorspacecpp11crayoncrosstalkcurldata.tabledigestdplyrdttenglishevaluatefansifarverfastmapfontawesomeforcatsfsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrisobandjaneaustenrjquerylibjsonliteknitrlabelinglaterlatticelazyevallexiconlifecyclemagrittrMASSMatrixmemoisemgcvmgsubmimemodeltoolsmunsellnlmeNLPopensslopenxlsxpillarpkgconfigplotlyprettyunitsprogresspromisespurrrqdapRegexR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangrmarkdownsassscalesslamSnowballCstringistringrsyssyuzhettextcleantextshapetibbletidyrtidyselecttidytexttinytextmtokenizerstopicmodelstzdbutf8vctrsviridisLitevroomwithrwordcloudxfunxml2yamlzipzoo

Citation

To cite package ‘miRetrieve’ in publications use:

Friedrich J, Hammes H, Krenning G (2021). miRetrieve: miRNA Text Mining in Abstracts. R package version 1.3.4, https://CRAN.R-project.org/package=miRetrieve.

Corresponding BibTeX entry: 

  @Manual{,
    title = {miRetrieve: miRNA Text Mining in Abstracts},
    author = {Julian Friedrich and Hans-Peter Hammes and Guido
      Krenning},
    year = {2021},
    note = {R package version 1.3.4},
    url = {https://CRAN.R-project.org/package=miRetrieve},
  }

Readme and manuals

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.

Getting Started

An online version with the most important functions of miRetrieve is available under https://miretrieve.shinyapps.io/miRetrieve/.

To install miRetrieve from CRAN, run

install.packages("miRetrieve")

Alternatively, you can also install miRetrieve from GitHub by running

install.packages("devtools")

devtools::install_github("JulFriedrich/miRetrieve",
        dependencies = TRUE,
        repos = "https://cran.r-project.org/")

miRetrieve is built around the idea of using field-specific PubMed abstracts from PubMed to characterize and analyze microRNAs in disease-related fields (e.g. "miRNAs in diabetes").

To get started, download a microRNA-related abstract from PubMed via Save - Format: PMID - Create file and load it into R using

df <- miRetrieve::read_pubmed("PubMed_file.txt")

and subsequently extract all microRNAs with

df <- extract_mir_df(df)

An extensive Vignette with the underlying mechanism, functions, and a complete workflow is available under

https://julfriedrich.github.io/miRetrieve/articles/miRetrieve.html

Authors

Julian Friedrich, Hans-Peter Hammes, Guido Krenning

License

miRetrieve is published under the GPL-3 license.

Publication

miRetrieve and its functions are presented in a manuscript, currently under review.

Supplementary Files referenced in the manuscript are located in a different repository, freely available under

https://github.com/JulFriedrich/miRetrieve-paper

Reference

Acknowledgments

  • join_mirtarbase is based on the latest miRTarBase version 8.0 (http://miRTarBase.cuhk.edu.cn/). 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.

  • compare_mir_terms_log2(), compare_mir_count_log2(), and compare_mir_terms_scatter() are greatly inspired by “tidytext: Text Mining and Analysis Using Tidy Data Principles in R.” by Silge and Robinson (https://www.tidytextmining.com/). In addition, "tidytext" provides a valuable resource of general text mining in R.

  • Key packages for miRetrieve are tidytext, topicmodels, and the packages included in the tidyverse (see Vignette).

Help Manual

Help pageTopics
Add topic column to data frameadd_col_topic
Keywords - animals.animal_keywords
Assign topics based on precalculated scoresassign_topic
Assign topics based on LDA modelassign_topic_lda
Keywords - biomarkers.biomarker_keywords
Calculate animal model scores for abstractscalculate_score_animals
Calculate biomarker scores for abstractscalculate_score_biomarker
Calculate patients scores for abstractscalculate_score_patients
Calculate scores of a self-chosen topiccalculate_score_topic
Combine data frames into one data framecombine_df
Combine miRNA vectors into onecombine_mir
Combine data frames containing stop wordscombine_stopwords
Compare count of miRNA names between different topicscompare_mir_count
Compare log2-frequency count of miRNA names between two topicscompare_mir_count_log2
Compare top count of unique miRNA names per topiccompare_mir_count_unique
Compare count of terms associated with a miRNA name over various topicscompare_mir_terms
Compare log2-frequency count of terms associated with a miRNA namecompare_mir_terms_log2
Compare shared terms associated with a miRNA namecompare_mir_terms_scatter
Compare terms uniquely associated with a miRNA namecompare_mir_terms_unique
Count miRNA names in a data framecount_mir
Count occurrence of miRNA names above thresholdcount_mir_threshold
Count SNPs in a data framecount_snp
Count targets in data framecount_target
Dataset of PubMed data of miRNAs in Colorectal Cancerdf_crc
miRTarBase version 8.0df_mirtarbase
Dataset of PubMed data of miRNAs in Pancreatic Cancerdf_panc
Test dataset of PubMed abstractsdf_test
Extract miRNA names from abstracts in data frameextract_mir_df
Extract miRNA names from stringextract_mir_string
Extract SNPs from abstracts in data frameextract_snp
Fit LDA-modelfit_lda
Generate data frame containing stop wordsgenerate_stopwords
Identify top miRNA names distinct for one topic compared to another topicget_distinct_mir_df
Identify miRNA names distinct for one vector compared to another vectorget_distinct_mir_vec
Get miRNA names from a data frameget_mir
Get PubMed-IDs of a data frameget_pmid
Get top miRNA names in common between two topics of a data frameget_shared_mir_df
Get miRNA names in common between two vectorsget_shared_mir_vec
Get SNPs from a data frameget_snp
Indicate if a miRNA name is contained in an abstractindicate_mir
Indicate if a term is contained in abstractsindicate_term
Add miRNA targets from miRTarBase version 8.0join_mirtarbase
Add miRNA targets from an xlsx-file to a data framejoin_targets
Stop words for n-gramsngram_stopwords
Keywords - patients.patients_keywords
Plot terms associated with LDA-fitted topicsplot_lda_term
Plot count of most frequently mentioned miRNA namesplot_mir_count
Plot occurrence count of miRNA names over different thresholdsplot_mir_count_threshold
Plot development of miRNA name mentioning over timeplot_mir_development
Plot number of newly mentioned miRNA names/yearplot_mir_new
Plot count of top terms associated with a miRNA nameplot_mir_terms
Plot perplexity score of various LDA modelsplot_perplexity
Plot frequency of animal model scores in abstractsplot_score_animals
Plot frequency of biomarker scores in abstractsplot_score_biomarker
Plot frequency of patient scores in abstractsplot_score_patients
Plot frequency of self-chosen topic scores in abstractsplot_score_topic
Plot count of miRNA targetsplot_target_count
Plot targets and corresponding miRNAs as a scatter plotplot_target_mir_scatter
Create wordcloud of terms associated with a miRNA nameplot_wordcloud
Convert PubMed-file from PubMed into a data frameread_pubmed
Convert JATS-file from PubMed into a data frameread_pubmed_jats
Save data frame(s) as xlsx-filesave_excel
Save the last generated figuresave_plot
Stop words for text mining with common PubMed 2-gramsstopwords_2gram
Stop words for text mining with miRetrievestopwords_miretrieve
Stop words for text mining from PubMed abstractsstopwords_pubmed
Subset data frame for a termsubset_df
Subset data frame for specific miRNA namessubset_mir
Subset data frame for miRNA names exceeding a thresholdsubset_mir_threshold
Subset data frame for abstracts of research articlessubset_research
Subset data frame for abstracts of review articlessubset_review
Subset data frame for specific SNPssubset_snp
Subset data frame for abstracts published in a specific periodsubset_year