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 |