Каталог навыков агентов

Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, popula...

Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS,...

Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-d...

Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (C...

Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) c...

Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseR...

Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV dete...

Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical sta...

Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of...

Identify recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat deconstructi...

Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenbe...

This skill should be used when the user needs to query COSMIC Cancer Gene Census to check if genes are known cancer gene...

Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threon...

Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classi...

Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV sca...

Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and t...

Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiple...

Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) wher...

Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CB...

Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Li & Hart 2019 Genome Med), a bidirectional Z-score met...

Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK ML...

Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Cover...

Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA log...

Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base...

Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condit...

Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each ce...

Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confound...

Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and S...

Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and...

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by e...

Build circular genome visualizations using circlize (R), pyCirclize (Python), or Circos (Perl CLI) with ideogram tracks,...

Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency sa...

Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method pr...

Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud pl...

Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or p...

Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias di...

Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotti...

Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scal...

Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scali...

Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for animat...

Plot per-gene mutation distributions on a protein-domain map (lollipop / needle plots) showing mutation position, recurr...

Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with co...

Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParam...

Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Pytho...

Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2,...

Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py w...

Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with e...

Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif,...

Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2-gr...

Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted threshold...

Fetches compound properties and species taxonomy from the official PubChem PUG-REST and NCBI Taxonomy APIs. Retrieves mo...

Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying signific...

Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visua...

Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of p...

Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 w...

Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, a...

Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-te...

Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT wi...

Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcu...

专门用于获取生物信息学工具文档（如 Bioconductor, CRAN, PyPI）的技能，具备处理特定领域文档站点的重定向、反爬及镜像切换能力。

Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant cal...

Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefacti...

Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indica...

Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 opt...

Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm...

Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (s...

Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP...

Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), varia...

Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetc...

Navigate between NCBI databases using Biopython's Entrez module (ELink utility).

Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to pr...

Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword,...

Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies...

Assigns isolate identity at the right resolution for the question -- ANI / Mash species triage, 7-locus MLST historical...

Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dyn...

Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017),...

Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json re...

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `ba...

Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected P...

Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Na...

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-a...

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scal...

Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, proc...

Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Be...

Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, met...

Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, re...

Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments...

Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or txi...

Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt,...

Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-r...

Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM,...

Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/d...

Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-qual...

Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequence...

Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element b...

Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM,...