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Claude Skills by BioTender-max
github.com/BioTender-max897 skills8 installs817 views
- Star AlignmentAlign RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.Votes: 0GitHub stars: 171
- Statistical AnalysisStatistical analysis for metabolomics data. Covers preprocessing (log2 transformation, normalization), limma moderated testing with empirical Bayes, Welch's t-tests with BH correction, fold change estimation, and multivariate methods (PCA, PLS-DA, OPLS-DA). Use when identifying differentially abundant metabolites or building classification models.Votes: 0GitHub stars: 171
- Structural AlignmentAlign protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.Votes: 0GitHub stars: 171
- Structural Variant CallingCall structural variants (SVs) from sequencing data using Manta, Delly, GRIDSS, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations too large for standard SNV callers. Use when detecting structural variants from short-read or long-read data and building consensus callsets.Votes: 0GitHub stars: 171
- Structure ProbingAnalyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucleotide reactivity profiles that constrain structure prediction. Use when processing SHAPE-MaP or DMS-MaPseq sequencing data to obtain experimental RNA structure information.Votes: 0GitHub stars: 171
- Subclonal Copy NumberResolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal C...Votes: 0GitHub stars: 171
- Subgroup AnalysisPerforms subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submission...Votes: 0GitHub stars: 171
- Substructure SearchSearches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.Votes: 0GitHub stars: 171
- Super EnhancersIdentifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers ...Votes: 0GitHub stars: 171
- Survival AnalysisPerforms time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival time (RMST) under non-PH, competing risks via Fine-Gray vs cause-specific Cox, weighted log-rank and MaxCombo for non-proportional hazards, recurrent events (Andersen-Gill, PWP, WLW), and interval-censored data. Use when analyzing time-to-event endpoints (OS, PFS, DOR, TTR, TTNT) in oncology or other clinical trials.Votes: 0GitHub stars: 171
- Synteny AnalysisDetect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting...Votes: 0GitHub stars: 171
- Bio Agent Skills HubDiscover and invoke 1,676 deduplicated biomedical AI agent skills from the Awesome Bio Agent Skills repository (20 source repos, 15 categories). Use this skill as a router whenever a user needs a bioinformatics/biomedical task (genomics, transcriptomics, single-cell, proteomics, protein design, clinical, epigenomics, multi-omics, pathway, metagenomics, database queries, visualization, workflows): search the index, locate the best-matching skill, fetch its SKILL.md, and follow it.Votes: 0GitHub stars: 171
- Atac SeqATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.Votes: 0GitHub stars: 171
- Bio Analysis System**Step 5: Analysis system design (分析方法体系构建)** Build the analysis layer for the manuscript by identifying which analyses, tools, and biological validations should support each figure and each task.Votes: 0GitHub stars: 171
- Bio Dataset Search**Step 3: Dataset search and task matching (数据集搜索与匹配)** Find suitable datasets for each task and map datasets to the task system defined earlier in the manuscript pipeline.Votes: 0GitHub stars: 171
- Bio Figure Design**Step 6: Figure design (Figure 详细设计)** Design the manuscript figures panel by panel, including the figure logic, panel content, and caption intent.Votes: 0GitHub stars: 171
- Bio Human Feedback**Phase 2.6: Human review checkpoint (人类反馈验证)** Present the refined proposal to a human reviewer, collect feedback, and decide whether to continue or loop back for revision.Votes: 0GitHub stars: 171
- Bio Innovation Check**Step 1: Innovation assessment (创新性检测)** Estimate whether a research idea is sufficiently novel for a strong methods-style paper by expanding the topic and searching the literature.Votes: 0GitHub stars: 171
- Bio Manuscript Pipeline**End-to-end pipeline from structured research input to a full manuscript plan (一条龙 Pipeline)** BioClaw integration notes: - This skill is staged under `container/skills/` as part of a multi-skill manuscript pipeline. - Shared templates and helper scripts are available under the sibling directory `bio-manuscript-common/`. - When this pipeline needs supporting capabilities, prefer the copied BioClaw sibling skills in `container/skills/` over any `~/.openclaw/...` layout assumptions. - This ski...Votes: 0GitHub stars: 171
- Bio Manuscript Refine**Refine loop: three-reviewer iterative refinement (三审稿人迭代优化)** Run a reviewer-style refinement loop over the manuscript plan using three perspectives: editor, computational reviewer, and biological reviewer.Votes: 0GitHub stars: 171
- Bio Manuscript Text**Step 7: Manuscript drafting (论文文案生成)** Draft the main manuscript text from the figure plan, metric system, and analysis system.Votes: 0GitHub stars: 171
- Bio Metric System**Step 4: Metric system design (评价指标体系构建)** Build a defensible set of quantitative and qualitative metrics by extracting them from related work or adapting them from adjacent fields.Votes: 0GitHub stars: 171
- Bio Ppt Generate**Presentation generation (组会汇报 PPT)** Generate a concise presentation package from the final proposal and demo / validation outputs.Votes: 0GitHub stars: 171
- Bio Task System**Step 2: Task system design (任务体系构建)** Identify the main task categories in the field and organize them into a staged difficulty ladder.Votes: 0GitHub stars: 171
- Bio ToolsBiology research tools reference. Always available inside agent containers.Votes: 0GitHub stars: 171
- Blast SearchRun BLAST sequence similarity searches. Use when the user asks to BLAST a sequence, find similar sequences, identify a gene/protein, or do homology search. Triggers on "blast", "sequence similarity", "homology", "identify sequence".Votes: 0GitHub stars: 171
- Cell AnnotationAutomated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.Votes: 0GitHub stars: 171
- Chip SeqChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.Votes: 0GitHub stars: 171
- Differential ExpressionBulk transcriptomics differential expression with count-aware modeling, design validation, contrast handling, thresholded exports, and publication-ready DE figures.Votes: 0GitHub stars: 171
- MetagenomicsShotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.Votes: 0GitHub stars: 171
- ProteomicsMass spectrometry proteomics QC, quantification, comparative analysis, and export for DDA, DIA, and protein-level result tables.Votes: 0GitHub stars: 171
- Query AlphafoldQuery AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".Votes: 0GitHub stars: 171
- Query ClinvarQuery ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".Votes: 0GitHub stars: 171
- Query EnsemblQuery Ensembl for genomic data. Use when user asks about gene coordinates, genomic sequences, variants, gene structure, exons, transcripts, or species comparison. Triggers on "ensembl", "gene coordinates", "genomic location", "exon", "transcript", "variant location", "rsid", "rs number".Votes: 0GitHub stars: 171
- Query GeoQuery NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on "geo", "gene expression omnibus", "expression dataset", "RNA-seq dataset", "microarray dataset", "GSE", "GDS".Votes: 0GitHub stars: 171
- Query InterproQuery InterPro for protein domains and families. Use when user asks about protein domains, functional sites, protein families, domain architecture, or motifs. Triggers on "interpro", "protein domain", "domain architecture", "protein family", "functional site", "motif".Votes: 0GitHub stars: 171
- Query KeggQuery KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Triggers on "kegg", "pathway", "metabolic pathway", "signaling pathway", "pathway genes".Votes: 0GitHub stars: 171
- Query OpentargetQuery OpenTargets for drug targets, disease associations, and therapeutic evidence. Use when user asks about drug targets, disease mechanisms, target validation, or drug-disease associations. Triggers on "opentarget", "drug target", "target validation", "disease association", "therapeutic target", "drug for disease".Votes: 0GitHub stars: 171
- Query PdbQuery RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".Votes: 0GitHub stars: 171
- Query ReactomeQuery Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details. Triggers on "reactome", "signaling cascade", "biological pathway", "pathway diagram", "reaction mechanism".Votes: 0GitHub stars: 171
- Query StringdbQuery STRING for protein-protein interactions. Use when user asks about protein interactions, interaction networks, binding partners, or interactome. Triggers on "string", "protein interaction", "interaction network", "binding partners", "interactome", "PPI".Votes: 0GitHub stars: 171
- Query UniprotQuery UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".Votes: 0GitHub stars: 171
- Report TemplatePublication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables, figure captions, callout boxes, and page headers/footers.Votes: 0GitHub stars: 171
- Scrna Preprocessing ClusteringStandard scRNA-seq preprocessing and clustering with Scanpy. Use for QC, normalization, HVG selection, PCA, neighbor graph construction, UMAP, Leiden clustering, and export of an analysis-ready AnnData object.Votes: 0GitHub stars: 171
- Sds Gel ReviewReview SDS-PAGE or protein purification gel images using DNA sequence, protein sequence, base-pair length, expected protein size, and lane labels. Use when the user wants to judge whether a gel ran well, whether the main band matches the expected product, or whether there may be impurities, degradation, aggregation, or low expression.Votes: 0GitHub stars: 171
- Sec ReportSEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and publication-quality PDF report generation via Typst templates. Triggers on "SEC", "size exclusion", "chromatography", "oligomer analysis", "protein assembly", "SEC report".Votes: 0GitHub stars: 171
- Sequence AnalysisAnalyze DNA/RNA/protein sequences. Use when the user provides a sequence and asks for analysis, translation, GC content, ORFs, motifs, restriction sites, or primer design. Triggers on "sequence", "translate", "GC content", "ORF", "primer", "restriction", "complement", "reverse complement".Votes: 0GitHub stars: 171
- Skills HubBrowse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks about available skills, advanced workflows, or specialized analysis pipelines. Triggers on "skills hub", "more skills", "install skill", "community skills", "find a skill for".Votes: 0GitHub stars: 171
- Structural BiologyStructure retrieval, confidence-aware AlphaFold DB usage, coordinate download, PAE and pLDDT interpretation, and structure-guided biological annotation.Votes: 0GitHub stars: 171
- Acmg ClassificationApplies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.Votes: 0GitHub stars: 171