Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation.
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses.
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information.
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information.
Computes DNA methylation age (DNAm age) and pace of aging by applying frozen elastic-net epigenetic clocks to a clean beta matrix with methylclock, dnaMethyAge, or methyl — from…
Designs and defends an epigenome-wide association study (EWAS) on 450K/EPIC array or bisulfite methylation - the layer deciding whether a hit is credible.
Tests which individual taxa differ between groups on an amplicon ASV/feature table (phyloseq) using compositionally-aware methods - ALDEx2 (Dirichlet-MC CLR, conservative),…
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables.
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables.
Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer…
Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA,…
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel.
Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception,…
Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautome — from…
Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows).
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public data — from…
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta…
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels.
Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation events, calibrating phylogenies with fossils, choosing between…
Designs and scaffolds bioinformatics pipelines using Prefect (Python) with Dask for local/distributed task execution and Nextflow for HPC scheduler-native execution.
Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assa — from…
Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity),…
Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction.
Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and DEqMS workflows with emp — from…
Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit…
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome. — from bg-szy/TOP-SKILLS
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample s — from…
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample s — from…
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is ne — from…
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is ne — from…
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill.
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of…
Tests whether a proposed or predicted RNA secondary structure is supported by evolutionary covariation using R-scape, which scores compensatory substitutions against a…
Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2.
Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot…
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython.
Performs molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar compounds using ECFP or MACCS keys and clusters molecules…
Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymm — from…
Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1…
Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR…
Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence score — from…
Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence score — from…
Detects putative ligand-binding pockets and druggable cavities de novo on an apo protein structure with fpocket, P2Rank, CASTp, and DoGSiteScorer, ranking them by…
Measures geometric properties of protein structures with Biopython Bio.PDB - interatomic distances, distance matrices, bond and dihedral angles (phi/psi/chi, Ramachandran),…
Maps protein-protein and protein-ligand interfaces with Bio.PDB, computing contact residues and buried surface area (BSA).
Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1.
Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1.
Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB. Use when choosing a format (mmCIF/PDBx vs legacy PDB vs BinaryCIF) for a structure that…
Modifies protein structures in place with Biopython Bio.PDB - transforms coordinates, strips waters/heteroatoms, overloads the B-factor column, renumbers, and builds entities.
Navigate the Bio.PDB SMCRA hierarchy (Structure-Model-Chain-Residue-Atom) safely, surfacing the heterogeneity it hides by default.
Prepares a deposited or predicted structure for docking, molecular dynamics, or electrostatics by adding hydrogens, assigning protonation and tautomer states, and filling missing…
Judges whether a macromolecular model (or a region of it) is reliable enough to build on, using resolution, R-free, B-factors, MolProbity geometry, and predicted-model confidence…
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matche — from…
Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector bindi — from…
Builds and simulates multi-species metabolic community models from member genome-scale models, using MICOM for abundance-weighted steady-state community FBA and cooperative…
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints.
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy.
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions.