Biology & Genomics

Build TCR clonotypes, diversity and lineages from repertoire FASTQ with MiXCR

Find temporal gene modules and pathway enrichment in bulk time-course data

Write FASTA, FASTQ, GenBank and EMBL sequence files with Biopython

Build and diagram SimBiology pharmacokinetic and biological models in MATLAB

Fit SimBiology model parameters to data and compute PK metrics like NCA

Simulate SimBiology ODE and stochastic models with scenarios and sensitivity analysis

Search bioRxiv preprints by keyword, author, date and category and download PDFs

Run initial single-cell and bioinformatics data analysis with QC and reports

Run QC, normalization and differential abundance on Olink and SomaScan proteomics data

Compute GC, ORFs, molecular weight and other metrics for a FASTA sequence file

Infer ancestry from consumer DNA files and compare ancestry-specific effect sizes

Detect Neanderthal and Denisovan DNA segments in modern human genomes

Fetch ArrayExpress study metadata, sample design and data files by accession

Find Bioconductor packages and generate starter code for a bioinformatics workflow

Run FastQC and MultiQC sequencing quality control with charts and an MCP server

Fetch BioStudies study metadata and download attached files by accession

Assess genome, transcriptome and protein completeness with BUSCO

Segment cells in fluorescence microscopy images and measure per-cell morphology

Score how specific a gene's expression is across cell types in a single-cell atlas

Trim and clean 16S and 18S amplicon reads so they are ready for DADA2

Run ancestry PCA against Simons Genome Diversity Project reference data

Profile shotgun metagenomes for taxonomy, resistance genes and pathways

Estimate methylation cycle activity and capacity from SNP genotype data

Rank CRISPR screen hits from guide-level count tables with deterministic scoring

Summarize differential expression results into ranked genes and biological themes

Predict gene expression from H&E tissue tiles for the genes you name

Run population genetics stats on aligned DNA or VCFs for diversity and neutrality

Analyze pooled viability screens and rank drug repurposing candidates

Look up ENA sequencing runs and download FASTQ files by accession

Fetch cis-eQTL statistics for a gene region from the EBI eQTL Catalogue

Compute genetic diversity and HEIM equity scores with FST and PCA plots

Build phylogenetic distance matrices and trees from VCF or FASTA data

Find causal variants at GWAS loci with SuSiE credible sets and posterior probabilities

Launch and monitor Flow.bio pipelines, samples and uploads through its API

Find, recommend and run Galaxy bioinformatics tools from usegalaxy.org

Compare your genome to the PGP-1 reference and estimate ancestry mix

Score genetic compatibility across male-female pairs in a Genomebook generation

Search NCBI GEO and download series metadata and data files by accession

Predict gene and transcript structure from a DNA sequence via a hosted API

Predict chromatin state, histone marks and TF binding from DNA sequences

Predict enhancer activity scores across windows of a DNA sequence

Predict tissue and cell-type gene expression from DNA near a transcription start site

Detect promoter regions in DNA sequences with a hosted transformer model

Detect splice donor and acceptor sites in DNA sequences with a hosted model

Fetch GWAS summary statistics for one genomic window from the GWAS Catalog

Look up a variant across eight genomic databases including GWAS Catalog and GTEx

Run an end-to-end GWAS with PLINK2 QC and REGENIE and plot the results

Calculate polygenic risk scores from consumer genetic data using PGS Catalog

Harmonize GWAS summary statistics from common tools into one canonical table