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Skills في هذا المستودع
جمع SkillsMP عدد ٢٣٦ من skills من BioTender-max/awesome-bio-agent-skills. افتح أي skill لمراجعة مصدره وتفاصيله.
BioTender-max/awesome-bio-agent-skillsعرض ٣٦ من أصل ٢٣٦ skills مجمعة.
Run a multi-agent scientific manuscript review with parallel specialist reviewers, disagreement checks, and an editor meta-review. Use when reviewing a manuscript, preprint, revision, or rebuttal in Codex or Claude Code.
لغة النص الأصلي: الإنجليزية
Author, execute, and deliver reproducible analysis notebooks in marimo (default) or Jupyter, with all cells run end-to-end and figures embedded. Also converts between marimo and Jupyter on request.
لغة النص الأصلي: الإنجليزية
Build production-ready Plotly Dash dashboards with consistent theming, clear layouts, and performant callbacks.
لغة النص الأصلي: الإنجليزية
Search the PMC Open Access literature with polars-dovmed. Author structured JSON queries directly, then use the hosted API when an API key is available or fall back to local dovmed scan over PMC, bioRxiv, or both parquet corpora.
لغة النص الأصلي: الإنجليزية
Structured, decision-ready review framework for AI/ML, computational biology, and bioscience proposals. Use when evaluating grant, project, or funding proposals.
لغة النص الأصلي: الإنجليزية
Assess paper and journal impact using OpenAlex citation counts, optional Altmetric data, and curated journal impact-factor references. Use when comparing papers, journals, or literature shortlists by reach and influence.
لغة النص الأصلي: الإنجليزية
Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.
لغة النص الأصلي: الإنجليزية
Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database;…
لغة النص الأصلي: الإنجليزية
Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for…
لغة النص الأصلي: الإنجليزية
Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use…
لغة النص الأصلي: الإنجليزية
Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network…
لغة النص الأصلي: الإنجليزية
Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for…
لغة النص الأصلي: الإنجليزية
Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs reference, segment with CBS/HMM, call amps/dels, scatter/diagram plots, purity/ploidy, VCF/SEG export. CLI plus Python API (cnvlib). Use…
لغة النص الأصلي: الإنجليزية
NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.
لغة النص الأصلي: الإنجليزية
Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for…
لغة النص الأصلي: الإنجليزية
Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings. Design novel proteins, extract ML features, or fold sequences. Local GPU or EvolutionaryScale Forge API. Use AlphaFold for traditional…
لغة النص الأصلي: الإنجليزية
GSEA and over-representation analysis (ORA) for RNA-seq and proteomics. Wraps Enrichr for ORA against MSigDB, KEGG, GO, and 200+ databases; runs preranked GSEA on ranked DE gene lists. Outputs enrichment tables and running-score plots. Use after DESeq2 or…
لغة النص الأصلي: الإنجليزية
NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats. Build PRS candidates, analyze pleiotropy, fetch stats for Manhattan plots. No auth.
لغة النص الأصلي: الإنجليزية
Harmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving biology. Run after PCA, before UMAP. Scales to millions of cells. Python (harmonypy, scanpy) and R (Seurat).
لغة النص الأصلي: الإنجليزية
Open-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via ontologies (Bionty), query datasets. Integrates with Nextflow, Snakemake, W&B, scVI. For scRNA-seq use scanpy; for ontology lookups use bionty.
لغة النص الأصلي: الإنجليزية
Research posters in LaTeX using beamerposter, tikzposter, or baposter. Layout, typography, color schemes, figure integration, accessibility, and QA for conferences. Includes templates. For figure generation use matplotlib-scientific-plotting or…
لغة النص الأصلي: الإنجليزية
MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter contaminants/decoys; log2 + median-normalize; impute MNAR; t-test with FDR; volcano plot; GO/pathway enrichment. Use Proteome Discoverer for…
لغة النص الأصلي: الإنجليزية
Molecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit 2D, Mordred), pretrained embeddings (ChemBERTa, GIN, Graphormer), pharmacophores. Scikit-learn compatible with parallelization/caching. For…
لغة النص الأصلي: الإنجليزية
Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by…
لغة النص الأصلي: الإنجليزية
Multi-modal single-cell analysis with muon/MuData. Joint RNA+ATAC (10x Multiome), CITE-seq (RNA+protein), other multi-omics. MuData holds per-modality AnnData with shared obs. WNN joint embedding, per-modality preprocessing, MOFA factor analysis. Use…
لغة النص الأصلي: الإنجليزية
Graph and network analysis toolkit. Four graph types (directed, undirected, multi-edge), centrality, shortest paths, community detection, generators, I/O (GraphML, GML, edge list), matplotlib viz. For large graphs (100K+ nodes) use igraph or graph-tool; for…
لغة النص الأصلي: الإنجليزية
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
لغة النص الأصلي: الإنجليزية
GWAS and population genetics tool. Processes PLINK (.bed/.bim/.fam), VCF, and BGEN; runs QC (MAF, HWE, missingness), IBD estimation, PCA, and linear/logistic regression GWAS. Outputs Manhattan-ready summary stats. Use regenie or SAIGE for biobanks (>100k…
لغة النص الأصلي: الإنجليزية
Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement…
لغة النص الأصلي: الإنجليزية
protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing. Public access free; auth needed for private or publishing. Pair with…
لغة النص الأصلي: الإنجليزية
Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required. Search by name/CID/SMILES/InChIKey/formula, retrieve properties (MW, XLogP, TPSA, H-bond counts), do similarity/substructure searches with…
لغة النص الأصلي: الإنجليزية
Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. Use for two-group comparisons, multi-factor designs with batch correction, multiple contrasts.
لغة النص الأصلي: الإنجليزية
scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.
لغة النص الأصلي: الإنجليزية
Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR…
لغة النص الأصلي: الإنجليزية
Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database for structures.
لغة النص الأصلي: الإنجليزية
Query ZINC15/ZINC22 virtual compound libraries (1.4B compounds, 750M purchasable). Search lead/fragment/drug-like compounds by MW, logP, reactivity, or SMILES similarity; download 3D sets for docking. For bioactivity use chembl-database-bioactivity; for…
لغة النص الأصلي: الإنجليزية