What you can do here
42 scientific analyses, each one run for you.
Every page is one job: what the work involves, the stages in order, what usually goes wrong, and the request that starts it. The research agent does it on a machine of its own — no install, no cluster, no GPU of your own.
Genomes and metagenomes
- Check genome assembly completeness onlineAssess the completeness of your genome assembly, transcriptome, or gene set with BUSCO 6.1.0 using curated OrthoDB 12 single-copy orthologues, without installing local tools or lineage datasets.
- Assemble a genome from sequencing readsAssemble genomes de novo using MaSuRCA from short paired-end reads alone or combined with long reads, then evaluate assembly contiguity and lineage-specific completeness with BUSCO.
- Recover genomes from a metagenomeRecover metagenome-assembled genomes from your contigs and read cohort using Bowtie 2, samtools, and MetaCAT, with lineage completeness and contamination checked by BUSCO.
- Predict genes in a bacterial genomePredict protein-coding genes in bacterial or archaeal assemblies with Prodigal, then annotate functions using DIAMOND or MMseqs2 homology searches against reference databases.
Viruses and CRISPR
- Annotate a phage genome onlineAnnotate bacteriophage contigs using Pharokka to identify protein-coding genes, PHROG functional categories, tRNAs, CRISPR arrays, and AMR or virulence markers.
- Find viruses and prophages in a genome or metagenomeIdentify viral contigs and integrated proviruses in assembled genomes or metagenomes using geNomad, then determine their completeness and contamination with CheckV.
- Check viral genome completeness and contaminationAssess viral genome completeness, host contamination and MIUViG quality tiers with CheckV. Establish whether your sequences represent complete genomes or fragments before downstream annotation.
- Classify a phage to ICTV genus and speciesClassify bacteriophage genomes to ICTV genus and species using taxmyPHAGE and the INPHARED database, applying the official 70% and 95% nucleotide identity thresholds.
- Find RNA viruses in metatranscriptome assembliesIdentify RNA viruses in metatranscriptome assemblies by screening for RdRp domains across eight profile HMM collections, with MMseqs2 taxonomy against RefSeq RNA viruses.
- Find CRISPR arrays and Cas genes in a genomeIdentify CRISPR arrays, predict Cas operons, and classify subtypes across bacterial, archaeal, or metagenomic assemblies without local software installation.
- Analyse a pooled CRISPR screenAnalyse pooled CRISPR knockout screens from sgRNA counts using MAGeCK, with gene ranking and honest false discovery rate correction across screening targets.
Sequencing data
- Differential expression from RNA-seq countsEstimate log fold changes and false discovery rates directly from unnormalised RNA-seq count matrices using negative binomial models with empirical Bayes shrinkage, batch adjustment, and stable gene identifier mapping.
- Run an nf-core pipeline without a clusterRun standard nf-core pipelines locally using Nextflow. Validate your samplesheet against the pinned pipeline schema, execute on a dedicated single-machine job, and inspect MultiQC reports without managing cluster queues.
- Call and filter variants from aligned readsCall, normalise, and filter genetic variants from aligned sequencing reads across explicit genome builds, generating standardised VCF records with calibrated population and functional effect annotations.
- Call peaks in ATAC-seq and ChIP-seq dataCall peaks from ATAC-seq and ChIP-seq alignments using MACS3, annotate genomic features with HOMER and bedtools, and query transcription-factor motifs against JASPAR.
- Quality-control and trim sequencing readsQuality-control, filter, and trim raw FASTQ files using fastp or Trimmomatic. Inspect quality reports, assess base scores and adapter contamination, and prepare clean reads for downstream analysis.
Single-cell and tissue
- Deconvolve bulk RNA-seq into cell typesEstimate cell-type proportions in bulk RNA-seq or Visium spots from an annotated single-cell reference using Rectangle, correcting for cell size differences and isolating uncharacterised signal as Unknown.
- Analyse single-cell RNA-seq dataProcess single-cell RNA-seq from raw counts through adaptive quality control, clustering, and cell-type annotation to pseudobulk differential expression across biological replicates.
- Analyse spatial transcriptomics dataAnalyse spatial transcriptomics data across sequencing and imaging platforms. Inspect QC, calculate spatially variable genes, map neighbourhoods, and deconvolve mixed spots using reference atlases.
- Quantify multiplexed tissue imagesQuantify multiplexed tissue sections into single-cell marker intensities, cell phenotypes, and spatial neighbourhood architectures using spatialproteomics without local software installation.
- Predict single-cell responses to unseen perturbationsPredict single-cell transcriptomic shifts under unmeasured perturbations, doses, or contexts using LabCompass flow matching models, evaluated directly against mean-shift and no-change baselines.
Proteins and structures
- Predict a protein structure from its sequencePredict or retrieve three-dimensional protein structures from sequence, evaluate per-residue pLDDT and inter-domain PAE confidence metrics, and identify disordered regions or experimental caveats.
- Dock a ligand into a protein onlineDock small molecules into prepared protein structures using AutoDock Vina, SMINA, DiffDock, or Boltz-2, with automatic control redocking and geometric sanity checks.
- Analyse a protein sequenceClean and characterise protein sequences, calculate physicochemical properties accurately, and identify domains and homologs using deterministic statistics, database queries, and sequence embeddings.
- Align sequences and build a phylogenetic treeClean sequence sets, align with MAFFT or MUSCLE, and infer maximum-likelihood phylogenetic trees using IQ-TREE or FastTree, with model selection and honest alignment metrics.
- Number, model and analyse antibodiesNumber antibody variable domains, annotate CDRs, generate 3D coordinates, and screen developability attributes using ANARCI, ImmuneBuilder, and sequence-based analysis tools without local installation.
Chemistry and compounds
- Calculate molecular properties from SMILESCalculate molecular descriptors and assess drug-likeness rules from SMILES. Receive standardised structures, physicochemical properties, and rule violations without local installations.
- Predict ADMET properties of a compoundStandardise small-molecule structures and predict 52 ADMET and toxicity endpoints using ADMET-AI and Chemprop D-MPNN ensembles, benchmarked against reference distributions of approved drugs.
- Screen a compound library against a targetScreen compound libraries against protein targets using AutoDock Vina, RDKit, and enrichment validation without local installation.
Instruments and measurements
- Build a PLS calibration from spectraBuild partial least squares calibrations from spectral matrices, assess predictive performance with robust cross-validation schemes, inspect VIP profiles, and resolve mixture spectra using MCR-ALS.
- Preprocess an untargeted LC-MS feature tableConvert an untargeted LC-MS feature table into an analysis-ready matrix using label-free diagnostics, blank and detection filtering, LOESS drift correction evaluated on held-out QCs, and matrix-specific normalisation.
- Process accelerometer data for sleep and activityExtract physical activity, rest-activity rhythms, and sleep estimates from raw wrist or hip accelerometer files using GGIR, configured for your study cohort.
- Segment organs and read findings in abdominal CTResearch reads of contrast-enhanced abdominal CT: 36 structures, organ volumes and finding scores, with the clinical line drawn.
- Fit dose-response and kinetics curvesFit enzyme kinetics and dose-response curves using lmfit and scipy. Obtain Km, Vmax, or IC50 with confidence intervals and residual plots from assay data without installing any software.
- Analyse flow cytometry dataParse FCS files, apply spillover compensation matrices, transform fluorescence scales, execute sequential gating from controls, and calculate population counts and parent frequencies.
- Quantify microscopy images and gelsQuantify raw intensity data from microscopy images, western blots, and colony plates without manual installation. Run background subtraction, segmentation, densitometry, and colocalisation using validated Python tools.
Literature and study design
- Run a literature review with citations you can checkSearch live scientific indexes, inspect methods in open-access full text, and build an evidence synthesis where every claim links directly to a retrieved citation.
- Design an experiment with the statistics settled firstTurn an open question into a staged, falsifiable protocol with sample size, randomisation, specific controls, and statistical analysis fixed before running an assay.
- Choose and check a statistical testChoose the correct statistical test directly from your experimental design, evaluate assumptions, and report effect sizes with confidence intervals rather than isolated p-values.
- Generate individual-level synthetic data from a summary tableGenerate an individual-level synthetic cohort matching summary statistics from a baseline table or dataset. You get a downloadable CSV and an itemised moment-by-moment verification report.
- Reproduce a published figure or benchmarkTest a specific published benchmark or quantitative figure by setting explicit tolerances beforehand, running the canonical code on isolated compute, and reporting an evidence-based verdict.
- Query scientific databases without an API keyQuery public scientific databases and datasets directly through an automated research agent. Retrieve verified records, explore schemas, and attribute every returned figure to its exact source without personal API keys.