Results for “genomebook”

Train unsupervised machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.

Query 20+ bioinformatics databases from the command line or Python for gene information, sequences, protein structures, enrichment analysis, and more.

Search, download, and extract public-domain books from Project Gutenberg. Look up books by ID or keyword via gutendex, download plain-text and EPUB editions, strip licensing boilerplate, extract clean text from EPUB for illustrated works, and classify fiction vs non-fiction. Ships a portable CLI script with zero external dependencies. Use when the user says "gutenberg", "public domain", "download a book", "classic literature", "free ebook", "gutenberg.org", or names any public-domain title or author.

Read, write, and manipulate genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.

Query 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome) with a unified Python interface for cross-database analysis, identifier mapping, and sequence analysis.

Takes pre-computed differential expression results from DESeq2, edgeR, limma, or PyDESeq2 and produces a structured, publication-ready summary with ranked gene lists, biological themes, and key observations.

Queries 9 genomic databases in parallel for a given rsID, returning unified GWAS, PheWAS, eQTL, and fine-mapping reports.

Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree, with visualization via ETE3 or FigTree for evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.

Query Google NotebookLM notebooks using Gemini's source-grounded answers. Automates browser-based authentication, notebook management, and question-answering workflows.