pku-yuangroup/openai4s

pku-yuangroup/openai4s · AGENTS.md

pku-yuangroup/openai4s · CLAUDE.md

pku-yuangroup/openai4s · skills/admet_genetic/SKILL.md · ADMET-guided genetic molecule optimization workflow from seed SMILES; use when the agent needs to build or run an…

pku-yuangroup/openai4s · skills/alphafold2/SKILL.md · Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022…

pku-yuangroup/openai4s · skills/audit-dataset/SKILL.md · Audit tabular datasets before analysis or training for schema drift, missing values, duplicate rows or IDs, target…

pku-yuangroup/openai4s · skills/bioprobench/SKILL.md · Score an LLM's biological-protocol reasoning on the BioProBench benchmark: protocol QA, step ordering, error detection…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-alignment-io/SKILL.md · Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-alignment-trimming/SKILL.md · Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-alignment-amplicon-clipping/SKILL.md · Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-alignment-filtering/SKILL.md · Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-alignment-indexing/SKILL.md · Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-alignment-sorting/SKILL.md · Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-alignment-validation/SKILL.md · Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-bam-statistics/SKILL.md · Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-duplicate-handling/SKILL.md · Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-pileup-generation/SKILL.md · Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-reference-operations/SKILL.md · Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-files-sam-bam-basics/SKILL.md · View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-msa-parsing/SKILL.md · Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-msa-statistics/SKILL.md · Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-multiple-alignment/SKILL.md · Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-pairwise-alignment/SKILL.md · Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences…

pku-yuangroup/openai4s · skills/bioskills/bio-alignment-structural-alignment/SKILL.md · Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-differential-splicing/SKILL.md · Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts)…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-isoform-switching/SKILL.md · Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-long-read-splicing/SKILL.md · Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-outlier-splicing-detection/SKILL.md · Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-sashimi-plots/SKILL.md · Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-single-cell-splicing/SKILL.md · Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-splice-variant-prediction/SKILL.md · Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-splicing-qc/SKILL.md · Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design…

pku-yuangroup/openai4s · skills/bioskills/bio-alternative-splicing-splicing-quantification/SKILL.md · Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-allele-specific-accessibility/SKILL.md · Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-atac-peak-calling/SKILL.md · Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-atac-qc/SKILL.md · ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-co-accessibility/SKILL.md · Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-consensus-peakset/SKILL.md · Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-deep-learning-atac/SKILL.md · Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer. Use when correcting Tn5 bias…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-differential-accessibility/SKILL.md · Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-enhancer-gene-linking/SKILL.md · Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-footprinting/SKILL.md · Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-motif-deviation/SKILL.md · Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-nucleosome-positioning/SKILL.md · Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC…

pku-yuangroup/openai4s · skills/bioskills/bio-atac-seq-single-cell-atac/SKILL.md · Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-colocalization-analysis/SKILL.md · Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-effector-gene-prioritization/SKILL.md · Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-fine-mapping/SKILL.md · Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-genetic-correlation/SKILL.md · Estimates bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-genomic-sem/SKILL.md · Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-heritability-partitioning/SKILL.md · Estimates SNP heritability and partitions it across functional annotations, cell types, and loci from GWAS summary…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-mediation-analysis/SKILL.md · Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-mendelian-randomization/SKILL.md · Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-pleiotropy-detection/SKILL.md · Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP)…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-proteome-mr-drug-target/SKILL.md · Runs cis-pQTL Mendelian randomization for drug-target validation using UKB-PPP (Olink), deCODE (SomaScan), Fenland…

pku-yuangroup/openai4s · skills/bioskills/bio-causal-genomics-transcriptome-wide-association/SKILL.md · Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-admet-prediction/SKILL.md · Predicts ADMET properties using ADMETlab 3.0 (119 platform features, including 77 prediction models with…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-conformer-generation/SKILL.md · Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-covalent-design/SKILL.md · Designs covalent inhibitors and warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-free-energy-calculations/SKILL.md · Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-generative-design/SKILL.md · Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-ml-docking-rescoring/SKILL.md · Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-molecular-descriptors/SKILL.md · Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6)…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-molecular-io/SKILL.md · Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-molecular-standardization/SKILL.md · Standardizes molecular structures using the ChEMBL structure pipeline for normalization and parent selection plus RDKit…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-pharmacophore-modeling/SKILL.md · Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-pose-validation/SKILL.md · Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-protac-degraders/SKILL.md · Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-qsar-modeling/SKILL.md · Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-reaction-enumeration/SKILL.md · Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-retrosynthesis/SKILL.md · Performs retrosynthetic planning using AiZynthFinder (template-based MCTS), maintained or version-pinned template-free…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-scaffold-analysis/SKILL.md · Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-shape-similarity/SKILL.md · Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-similarity-searching/SKILL.md · Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-substructure-search/SKILL.md · Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS…

pku-yuangroup/openai4s · skills/bioskills/bio-chemoinformatics-virtual-screening/SKILL.md · Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-allele-specific-binding/SKILL.md · Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-chip-deep-learning/SKILL.md · Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-chipseq-qc/SKILL.md · Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-chipseq-visualization/SKILL.md · Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare)…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-chromatin-state-segmentation/SKILL.md · Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-cut-and-run-tag/SKILL.md · Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-differential-binding/SKILL.md · Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows)…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-motif-analysis/SKILL.md · Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-peak-annotation/SKILL.md · Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-peak-calling/SKILL.md · Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-spike-in-normalization/SKILL.md · Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E…

pku-yuangroup/openai4s · skills/bioskills/bio-chip-seq-super-enhancers/SKILL.md · Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-adaptive-designs/SKILL.md · Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-bayesian-trials/SKILL.md · Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-categorical-tests/SKILL.md · Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-cdisc-data-handling/SKILL.md · Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-effect-measures/SKILL.md · Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-logistic-regression/SKILL.md · Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-missing-data-sensitivity/SKILL.md · Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-multiplicity-graphical/SKILL.md · Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel)…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-power-and-sample-size/SKILL.md · Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-subgroup-analysis/SKILL.md · Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-survival-analysis/SKILL.md · Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-biostatistics-trial-reporting/SKILL.md · Prepares statistical reports for clinical trials following CONSORT 2025, SPIRIT 2025, ICH E9(R1) estimands, and FDA…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-acmg-classification/SKILL.md · Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-clinvar-lookup/SKILL.md · Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-dbsnp-queries/SKILL.md · Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-gnomad-frequencies/SKILL.md · Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-hla-typing/SKILL.md · 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…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-msi-detection/SKILL.md · Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware)…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-myvariant-queries/SKILL.md · Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-pharmacogenomics/SKILL.md · Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-polygenic-risk/SKILL.md · Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-somatic-signatures/SKILL.md · Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 CN / 16 SV) from somatic VCFs…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-tumor-mutational-burden/SKILL.md · Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations…

pku-yuangroup/openai4s · skills/bioskills/bio-clinical-databases-variant-prioritization/SKILL.md · Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-ago-clip-mirna-targets/SKILL.md · Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse)…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-binding-site-annotation/SKILL.md · Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-clip-alignment/SKILL.md · Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-clip-deep-learning/SKILL.md · Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-clip-motif-analysis/SKILL.md · Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-clip-peak-calling/SKILL.md · Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-clip-preprocessing/SKILL.md · Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-clip-qc/SKILL.md · Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-crosslink-site-detection/SKILL.md · Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS)…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-differential-clip/SKILL.md · Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-m6a-clip/SKILL.md · Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 +…

pku-yuangroup/openai4s · skills/bioskills/bio-clip-seq-stamp-antibody-free/SKILL.md · Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-ancestral-reconstruction/SKILL.md · Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-comparative-annotation-projection/SKILL.md · Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-gene-family-evolution/SKILL.md · Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-gene-tree-species-tree-reconciliation/SKILL.md · Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-genome-distance-and-species-delineation/SKILL.md · Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-hgt-detection/SKILL.md · Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-introgression-detection/SKILL.md · Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics)…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-ortholog-inference/SKILL.md · Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology)…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-pangenome-analysis/SKILL.md · Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-positive-selection/SKILL.md · Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-synteny-analysis/SKILL.md · Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-whole-genome-alignment/SKILL.md · Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA)…

pku-yuangroup/openai4s · skills/bioskills/bio-comparative-genomics-whole-genome-duplication/SKILL.md · Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024)…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-allele-specific-copy-number/SKILL.md · Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-cnv-annotation/SKILL.md · Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-cnv-visualization/SKILL.md · Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-cnvkit-analysis/SKILL.md · Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-copy-ratio-segmentation/SKILL.md · Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-focal-amplification-ecdna/SKILL.md · Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB)…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-gatk-cnv/SKILL.md · Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-germline-cnv-interpretation/SKILL.md · Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-hrd-scoring/SKILL.md · Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-recurrent-cnv/SKILL.md · Identify recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat…

pku-yuangroup/openai4s · skills/bioskills/bio-copy-number-subclonal-copy-number/SKILL.md · Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-bagel-essentiality/SKILL.md · Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-base-editing-analysis/SKILL.md · Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-batch-correction/SKILL.md · Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-combinatorial-screens/SKILL.md · Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-copy-number-correction/SKILL.md · Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov)…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-crispresso-editing/SKILL.md · Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR)…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-drugz-chemogenomic/SKILL.md · Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Colic et al. 2019 Genome Med), a bidirectional Z-score…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-hit-calling/SKILL.md · Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-in-vivo-screens/SKILL.md · Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-jacks-analysis/SKILL.md · Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-library-design/SKILL.md · Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-mageck-analysis/SKILL.md · Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-perturb-seq-analysis/SKILL.md · Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-prime-editing-screens/SKILL.md · Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander…

pku-yuangroup/openai4s · skills/bioskills/bio-crispr-screens-screen-qc/SKILL.md · Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-circos-plots/SKILL.md · Build circular genome visualizations using circlize (R), pyCirclize (Python), or Circos (Perl CLI) with ideogram…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-color-palettes/SKILL.md · Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-dimensionality-reduction-plots/SKILL.md · Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-distribution-plots/SKILL.md · Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-flow-and-transition-plots/SKILL.md · Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-forest-funnel-plots/SKILL.md · Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-genome-tracks/SKILL.md · Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-ggplot2-fundamentals/SKILL.md · Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries +…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-heatmaps-clustering/SKILL.md · Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-interactive-visualization/SKILL.md · Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-lollipop-protein-maps/SKILL.md · Plot per-gene mutation distributions on a protein-domain map (lollipop / needle plots) showing mutation position…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-manhattan-qq-locuszoom/SKILL.md · Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-matplotlib-fundamentals/SKILL.md · Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-multipanel-figures/SKILL.md · Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-network-visualization/SKILL.md · Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-oncoprint-mutation-matrices/SKILL.md · Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-sequence-logos/SKILL.md · Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-statistical-annotation/SKILL.md · Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-upset-plots/SKILL.md · Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern…

pku-yuangroup/openai4s · skills/bioskills/bio-data-visualization-volcano-and-ma-plots/SKILL.md · Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-batch-downloads/SKILL.md · Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-biomart-queries/SKILL.md · Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-blast-searches/SKILL.md · Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-ensembl-rest/SKILL.md · Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara)…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-entrez-fetch/SKILL.md · Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-entrez-link/SKILL.md · Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-entrez-search/SKILL.md · Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-geo-data/SKILL.md · Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-interaction-databases/SKILL.md · Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-local-blast/SKILL.md · Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-ncbi-datasets-cli/SKILL.md · Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-ortholog-inference/SKILL.md · Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-remote-homology/SKILL.md · Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-sra-data/SKILL.md · Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror…

pku-yuangroup/openai4s · skills/bioskills/bio-database-access-uniprot-access/SKILL.md · Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms…

pku-yuangroup/openai4s · skills/bioskills/bio-differential-expression-batch-correction/SKILL.md · Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for…

pku-yuangroup/openai4s · skills/bioskills/bio-differential-expression-de-results/SKILL.md · Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of…

pku-yuangroup/openai4s · skills/bioskills/bio-differential-expression-de-visualization/SKILL.md · Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2…