Навыков: 36 916. Сортировка по числу звёзд.
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...
Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating...
Build marker gene alignments and phylogenetic trees.
Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spe...
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes...
Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing...
Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce s...
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, si...
Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use w...
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effe...
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using txim...
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use whe...
Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor inter...
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PC...
Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types....
Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamental...
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific cons...
Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miR...
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and...
Aggregate results, train ML models, and produce reports with validated references.
Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins withou...
Structure prediction and structure-based annotation.
Clusters genes by temporal expression profile shape using Mfuzz soft clustering, TCseq, and DEGreport degPatterns. Group...
Models continuous temporal trajectories from bulk or time-resolved omics data using generalized additive models (mgcv),...
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predic...
Normalize indel representation, decompose MNPs, and split multiallelic variants using bcftools norm. Use when comparing...
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting sp...
Detect, classify, and QC viral contigs.
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing w...
End-to-end genome annotation pipeline from assembled contigs to functional annotation, covering repeat masking, gene pre...
Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather...
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and associat...
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with m...
Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots...
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken...
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, meth...
End-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding p...
End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, var...
End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis...
Use this agent when you need to perform custom bioinformatics analyses on genes or proteins that go beyond standard data...
This skill should be used when conducting bioinformatics research, planning experiments, running analyses, or managing s...
Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, an...
Use when evaluating biological relevance, methodological appropriateness, or scientific validity of bioinformatics appro...
Comprehensive biology expert from molecular biology to ecology, covering cell biology, genetics, evolution, and physiolo...
Ralph-Inspired Adaptive Learning Framework for iterative, quality-gated biomarker report analysis
End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection wit...
---name: biomcp-server