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…