add_col_topic           Add topic column to data frame
animal_keywords         Keywords - animals.
assign_topic            Assign topics based on precalculated scores
assign_topic_lda        Assign topics based on LDA model
biomarker_keywords      Keywords - biomarkers.
calculate_score_animals
                        Calculate animal model scores for abstracts
calculate_score_biomarker
                        Calculate biomarker scores for abstracts
calculate_score_patients
                        Calculate patients scores for abstracts
calculate_score_topic   Calculate scores of a self-chosen topic
combine_df              Combine data frames into one data frame
combine_mir             Combine miRNA vectors into one
combine_stopwords       Combine data frames containing stop words
compare_mir_count       Compare count of miRNA names between different
                        topics
compare_mir_count_log2
                        Compare log2-frequency count of miRNA names
                        between two topics
compare_mir_count_unique
                        Compare top count of unique miRNA names per
                        topic
compare_mir_terms       Compare count of terms associated with a miRNA
                        name over various topics
compare_mir_terms_log2
                        Compare log2-frequency count of terms
                        associated with a miRNA name
compare_mir_terms_scatter
                        Compare shared terms associated with a miRNA
                        name
compare_mir_terms_unique
                        Compare terms uniquely associated with a miRNA
                        name
count_mir               Count miRNA names in a data frame
count_mir_threshold     Count occurrence of miRNA names above threshold
count_snp               Count SNPs in a data frame
count_target            Count targets in data frame
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
extract_mir_df          Extract miRNA names from abstracts in data
                        frame
extract_mir_string      Extract miRNA names from string
extract_snp             Extract SNPs from abstracts in data frame
fit_lda                 Fit LDA-model
generate_stopwords      Generate data frame containing stop words
get_distinct_mir_df     Identify top miRNA names distinct for one topic
                        compared to another topic
get_distinct_mir_vec    Identify miRNA names distinct for one vector
                        compared to another vector
get_mir                 Get miRNA names from a data frame
get_pmid                Get PubMed-IDs of a data frame
get_shared_mir_df       Get top miRNA names in common between two
                        topics of a data frame
get_shared_mir_vec      Get miRNA names in common between two vectors
get_snp                 Get SNPs from a data frame
indicate_mir            Indicate if a miRNA name is contained in an
                        abstract
indicate_term           Indicate if a term is contained in abstracts
join_mirtarbase         Add miRNA targets from miRTarBase version 8.0
join_targets            Add miRNA targets from an xlsx-file to a data
                        frame
ngram_stopwords         Stop words for n-grams
patients_keywords       Keywords - patients.
plot_lda_term           Plot terms associated with LDA-fitted topics
plot_mir_count          Plot count of most frequently mentioned miRNA
                        names
plot_mir_count_threshold
                        Plot occurrence count of miRNA names over
                        different thresholds
plot_mir_development    Plot development of miRNA name mentioning over
                        time
plot_mir_new            Plot number of newly mentioned miRNA names/year
plot_mir_terms          Plot count of top terms associated with a miRNA
                        name
plot_perplexity         Plot perplexity score of various LDA models
plot_score_animals      Plot frequency of animal model scores in
                        abstracts
plot_score_biomarker    Plot frequency of biomarker scores in abstracts
plot_score_patients     Plot frequency of patient scores in abstracts
plot_score_topic        Plot frequency of self-chosen topic scores in
                        abstracts
plot_target_count       Plot count of miRNA targets
plot_target_mir_scatter
                        Plot targets and corresponding miRNAs as a
                        scatter plot
plot_wordcloud          Create wordcloud of terms associated with a
                        miRNA name
read_pubmed             Convert PubMed-file from PubMed into a data
                        frame
read_pubmed_jats        Convert JATS-file from PubMed into a data frame
save_excel              Save data frame(s) as xlsx-file
save_plot               Save the last generated figure
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
subset_df               Subset data frame for a term
subset_mir              Subset data frame for specific miRNA names
subset_mir_threshold    Subset data frame for miRNA names exceeding a
                        threshold
subset_research         Subset data frame for abstracts of research
                        articles
subset_review           Subset data frame for abstracts of review
                        articles
subset_snp              Subset data frame for specific SNPs
subset_year             Subset data frame for abstracts published in a
                        specific period
