Biology & Genomics

Simulate growth, flux and gene knockouts in metabolic models with COBRApy

Plan shared-biomarker studies that link two comorbid diseases through DEGs and hub genes

Plan network toxicology studies comparing two exposures through shared target analysis

Find stable sample subtypes from bulk expression with consensus clustering and CDF plots

Plan non-oncology hub gene studies from multi-dataset transcriptome integration

Plan tumor transcriptome studies for prognostic biomarkers and hub genes

Download COSMIC somatic mutation data and cancer gene census for genomic analysis

Find essential and hit genes in pooled CRISPR screens with RRA analysis

Plan studies linking two diseases through shared DEGs, PPI hubs and diagnostic biomarkers

Query CTD for chemical, gene, disease and pathway interactions in toxicogenomics

Parse and standardize SMILES and compute descriptors and fingerprints with datamol

Convert BAM to bigWig and plot QC and heatmaps for ChIP-seq and ATAC-seq

Screen differentially expressed genes between two groups with volcano and heatmap plots

Predict blind ligand-protein binding poses with DiffDock and confidence scores

Find differentially expressed genes in RNA-seq or microarray data with volcano plots

Map disease mechanisms from molecules and pathways to clinical phenotypes

Design drug repurposing studies that link mechanisms, targets and validation routes

Organize drug, target and pathway evidence across tractability, clinical stage and crowding

Parse DrugBank XML for drug properties, targets, interactions and pathways

Plan two-disease transcriptome studies with shared biomarkers and hub genes

Plan shared-gene transcriptomic and machine learning studies for two diseases

Search the European Nucleotide Archive for sequences, FASTQ reads and metadata

Search ENCODE biosamples, experiments and objects by keyword or accession ID

Look up ENCORI miRNA-target and RNA-RNA regulatory interactions

Look up Ensembl genes, sequences and variant effects through the REST API

Compute ESTIMATE immune and stromal scores with heatmaps and group boxplots

Analyze and draw phylogenetic trees and NCBI taxonomy with the ETE toolkit

Interpret FastQC reports for RNA-seq, DNA-seq and ChIP-seq and fix quality issues

Parse FCS flow cytometry files into NumPy arrays and CSV tables

Look up NCBI Gene records for symbols and IDs with GO terms and phenotypes

Pull gene summaries, PubMed counts and transcripts for single genes or lists

Normalize expression matrices with log2, z-score or min-max scaling before analysis

Map gene structure and exon layouts for analysis and publication figures

Plan phenotype scoring studies that intersect gene signatures with DEGs and outcomes

Search NCBI GEO for expression datasets by keyword, organism or author

Query 20+ bioinformatics databases by gene or protein ID from a CLI or Python

Run GO and KEGG enrichment on a gene list and plot a combined dot chart

Run GSEA on a ranked gene list and produce enrichment tables and plots

Run GSVA or ssGSEA pathway analysis on expression data and plot a heatmap

Run fast genomic interval overlaps, coverage tracks and tokenization in Rust

Look up official gene symbols, names and identifiers in HGNC

Search the Human Metabolome Database for metabolites and extract their clinical data

Draft IACUC animal research protocols with a 3Rs justification

Run immune pathway GSVA or ssGSEA with Reactome gene sets and export a heatmap

Search JASPAR transcription factor binding matrices and retrieve PFM and PWM profiles

Retrieve KEGG genes, pathways, compounds and drugs through the KEGG API

Query KEGG pathways, genes and compounds over direct REST calls and map IDs

Calculate dilutions and solution recipes with step-by-step lab prep protocols

Track, query and version biological datasets and analyses with LaminDB