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miRetrieve  

miRNA Text Mining in Abstracts
View on CRAN: Click here


Download and install miRetrieve package within the R console
Install from CRAN:
install.packages("miRetrieve")

Install from Github:
library("remotes")
install_github("cran/miRetrieve")

Install by package version:
library("remotes")
install_version("miRetrieve", "1.3.4")



Attach the package and use:
library("miRetrieve")
Maintained by
Julian Friedrich
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-07-15
Latest Update: 2021-09-18
Description:
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
How to cite:
Julian Friedrich (2021). miRetrieve: miRNA Text Mining in Abstracts. R package version 1.3.4, https://cran.r-project.org/web/packages/miRetrieve
Previous versions and publish date:
1.3.0 (2021-07-15 13:30), 1.3.2 (2021-08-13 09:30)
Other packages that cited miRetrieve R package
View miRetrieve citation profile
Other R packages that miRetrieve depends, imports, suggests or enhances
Functions, R codes and Examples using the miRetrieve R package
Some associated functions: add_col_topic . animal_keywords . assign_topic . assign_topic_lda . biomarker_keywords . calculate_score_animals . calculate_score_biomarker . calculate_score_patients . calculate_score_topic . combine_df . combine_mir . combine_stopwords . compare_mir_count . compare_mir_count_log2 . compare_mir_count_unique . compare_mir_terms . compare_mir_terms_log2 . compare_mir_terms_scatter . compare_mir_terms_unique . count_mir . count_mir_threshold . count_snp . count_target . df_crc . df_mirtarbase . df_panc . df_test . extract_mir_df . extract_mir_string . extract_snp . fit_lda . generate_stopwords . get_distinct_mir_df . get_distinct_mir_vec . get_mir . get_pmid . get_shared_mir_df . get_shared_mir_vec . get_snp . indicate_mir . indicate_term . join_mirtarbase . join_targets . ngram_stopwords . patients_keywords . plot_lda_term . plot_mir_count . plot_mir_count_threshold . plot_mir_development . plot_mir_new . plot_mir_terms . plot_perplexity . plot_score_animals . plot_score_biomarker . plot_score_patients . plot_score_topic . plot_target_count . plot_target_mir_scatter . plot_wordcloud . read_pubmed . read_pubmed_jats . save_excel . save_plot . stopwords_2gram . stopwords_miretrieve . stopwords_pubmed . subset_df . subset_mir . subset_mir_threshold . subset_research . subset_review . subset_snp . subset_year . 
Some associated R codes: animals_score.R . assign_topic.R . biomarker_score.R . combine_mir.R . compare_mir_count.R . compare_mir_terms.R . count_mir_perc_total_threshold_helper.R . count_mir_single_topic.R . count_mir_threshold.R . detect_single_term.R . df_crc.R . df_mirtarbase.R . df_operations_combine_addtopic_subsetmir.R . df_panc.R . df_test.R . distinct_shared_mir.R . extract_mir.R . generate_stopwords.R . get_mir_vec.R . get_pmid.R . globals.R . helper_calculate_score.R . helper_control_shared_mir.R . join_mirtarbase.R . join_targets.R . lda_miretrieve.R . load_and_save_files.R . mirna_year_new_and_trend.R . patients_score.R . polymorphism.R . prepare_make_dtm_helper.R . pretty_breaks_helper.R . self_made_topics.R . stopwords_doc.R . stopwords_ngram_roxygen.R . subset_articles_review_year.R . subset_mir.R . target_mirna.R . tfidf_words.R . top_words_count_words_helper.R . wordcloud.R .  Full miRetrieve package functions and examples
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