Навыки: Данные

Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, ME...

Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input contro...

Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretatio...

Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representa...

Calls HLA class I and class II alleles at 2/4/6/8-field resolution from WGS/WES/RNA-seq/long-read data using OptiType, H...

Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware),...

Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, BridgePRS...

Extracts and assigns COSMIC v3.4 mutational signatures (84 SBS / 11 DBS / 18 ID / 24 CN / 16 SV) from somatic VCFs using...

Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-...

Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous ph...

Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when...

Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2...

Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via...

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

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

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

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

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

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 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...

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,...

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

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

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

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

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

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

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

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

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

Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.

Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarg...

Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNO...

Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-complia...

Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a sing...

Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test again...

Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray...

Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath,...

Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, buildin...

Evaluates scientific research rigor using systematic frameworks. Assesses methodology, statistics, biases, and evidence...

Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RN...

Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitizatio...

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...

KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metab...