В каталоге 183 730 навыков в 14 категориях.
Assigns honest lipid annotation levels, designs class-based internal-standard quantification, and runs lipid-aware diffe...
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipid...
Turns untargeted LC-MS/MS features (m/z, RT, MS/MS) into confidence-stratified metabolite annotations using spectral-lib...
Runs the MS-DIAL preprocessing workflow (peak picking, MS2Dec spectral deconvolution, alignment, gap-filling) and import...
Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing valu...
Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA), mu...
Decision-grade statistical analysis for metabolomics intensity tables. Covers transformation and scaling (Pareto vs unit...
Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution in...
Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking r...
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to spec...
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resi...
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene...
Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Us...
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade...
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor...
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots...
Detects cancer and infers tissue-of-origin from cfDNA methylation by choosing conversion chemistry (bisulfite vs EM-seq...
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files...
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for...
Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-...
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying...
Designs and defends an epigenome-wide association study (EWAS) on 450K/EPIC array or bisulfite methylation - the layer d...
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and...
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering...
Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsL...
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample di...
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundan...
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in prove...
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (D...
Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) a...
Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Ope...
Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitizatio...
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription fa...
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature...
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for...
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view...
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a...
Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembl...
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning...
Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Ort...
Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomi...
Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs,...
Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clus...
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enr...
Tests a ranked gene vector for coordinated expression shifts in GO, KEGG, Reactome, or MSigDB gene sets with clusterProf...
Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coord...
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metab...
Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-revi...
WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated...
Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and...
Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloadin...
Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding...
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, a...
Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2...
Frames the phasing/imputation pipeline before any tool runs: phasing and imputation are one Li-Stephens copying HMM (rec...
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, h...
Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosom...
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels....
Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics...
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creatin...
Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation eve...
Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-NG with expert model selection, branch support asse...
Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use whe...
Read, write, and convert phylogenetic tree files with Biopython Bio.Phylo, and choose an annotation-preserving parser (t...
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or...
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD me...
Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating...
Build marker gene alignments and phylogenetic trees.
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling,...
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using...
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify hap...
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/B...
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, as...
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics...
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate pop...
Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantificatio...
Designs and scaffolds bioinformatics pipelines using Prefect (Python) with Dask for local/distributed task execution and...
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, an...
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculat...
Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and h...
Rewrites your bio, name field and pinned-reel order to convert profile visits into follows and clicks. Use when the user...
Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM...
Cluster proteins into orthogroups and derive pangenome matrices.
Loads mass-spectrometry data into Python/R and strips the search engine's bookkeeping before any number is trusted -- re...
Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant prote...
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrom...
Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation,...
Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spe...
Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides....
Quality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream analys...
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localiz...
Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT,...
Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DI...
Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian pr...
Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with expli...
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, A...
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short...
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too hi...
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice ju...
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Il...