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:
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 = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- df_crc - Dataset of PubMed data of miRNAs in Colorectal Cancer
- df_mirtarbase - MiRTarBase version 8.0
- df_panc - Dataset of PubMed data of miRNAs in Pancreatic Cancer
- df_test - Test dataset of PubMed abstracts
- ngram_stopwords - Stop words for n-grams
- stopwords_2gram - Stop words for text mining with common PubMed 2-grams
- stopwords_miretrieve - Stop words for text mining with miRetrieve
- stopwords_pubmed - Stop words for text mining from PubMed abstracts
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:1abaa407f9. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 15 2024 |
R-4.5-linux | OK | Dec 15 2024 |
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