Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods.
Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery.
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants.
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants.
Cleans a shotgun metagenome of everything that is not the target community before profiling - host-read depletion (Hostile, bowtie2/T2T-CHM13), reagent/kitome contamination…
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from met — from…
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from met — from…
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation.
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.
Turns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi (RGChannelSet -> MethylSet ->…
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.
Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices.
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation diffe — from…
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation diffe — from…
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.
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons.
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons.
Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2.
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…
Chooses the enrichment generation before any tool runs, mapping the input shape to a method class - a pre-selected gene list plus a background to over-representation analysis…
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression — from…
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression — from…
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…
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLI — from…
Gene and region-based rare-variant aggregation - burden/collapsing, SKAT, SKAT-O, ACAT-V/ACAT-O, annotation-weighted STAAR - with regenie (--vc-tests), SAIGE-GENE+, and t — from…
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using Genot — from…
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics.
Designs and scaffolds bioinformatics pipelines using Prefect (Python) with Dask for local/distributed task execution and Nextflow for HPC scheduler-native execution.
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations.
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.
Builds publication-ready tables - descriptive Table 1, regression and differential-expression result tables, and supplementary tables - with gtsummary, gt, flextable, and…
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
Strategic scientific problem selection, project ideation, and troubleshooting based on the Fischbach & Walsh framework.
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…