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 |