Welcome to BRAD: Bioinformatics Retrieval Augmented Data’s documentation!
Contents:
- About BRAD
- Interface
- Core Modules
- Large Language Models
- Logging
- Utilities
- Scope
- Available Methods
add_output_file_path_to_string()
compile_latex_to_pdf()
delete_dirs_without_log()
ensure_directory_exists()
fieldSelectorFromDataFrame()
find_integer_in_string()
loadFromFile()
load_file_to_dataframe()
makeNamesConsistent()
outputFiles()
outputFromPriorStep()
pdfDownloadPath()
save()
savefig()
word_similarity()
- Planner
- Routing
- Prompt Templates
fieldChooserTemplate()
fileChooserTemplate()
geneDatabaseCallerTemplate()
getDefaultContext()
getPythonEditingTemplate()
historyChatTemplate()
matlabPromptTemplate()
plannerEditingTemplate()
plannerTemplate()
plannerTemplateForLibrarySelection()
pythonPromptTemplate()
pythonPromptTemplateWithFiles()
rerouteTemplate()
scrapeTemplate()
scriptSelectorTemplate()
setReportTitleTemplate()
summarizeAnalysisPipelineTemplate()
summarizeDatabaseCallerTemplate()
summarizeDocumentTemplate()
summarizeRAGTemplate()
- Tool Modules
- Lab Notebook
- Key Functions
- Available Methods
adj_matrix_builder()
best_match()
contextualCompression()
create_database()
cut()
documentEnrichment()
getDocumentSimilarity()
getInputDocumentJSONs()
getPreviousInput()
get_all_sources()
get_wordnet_pos()
normalize_adjacency_matrix()
pagerank_rerank()
pagerank_weighted()
queryDocs()
relative_frequency_of_char()
remove_repeats()
retrieval()
- Digital Library
- Literature Repositories
arxiv()
arxiv_scrape()
arxiv_search()
biorxiv()
biorxiv_real_search()
create_db()
parse_llm_response()
pubmed()
result_set_to_string()
search_pubmed_article()
updateDatabase()
webScraping()
- Bioinformatics Database
geneDBRetriever()
getTablesFormatting()
parse_llm_response()
- Enrichr
queryEnrichr()
- Gene Ontology (GO)
annotations()
chartGO()
fetch_annotation()
geneOntology()
goSearch()
pubmedPaper()
textGO()
- Software
- Lab Notebook
- Software Installation and Requirements