@aipoch
组织
We build insight moment for scientific research
324 个技能2 个仓库 7315
Run demanding scientific work on SSH compute hosts using direct execution or Slurm, a cluster job scheduler. Choose an enabled host, submit background jobs, check progress, collect outputs, and continue with analysis and artifact publication.
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This skill is applicable when using LaminDB. LaminDB is an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR-compliant. It is suitable for managing biological datasets (scRNA-seq, spatial transcriptomics, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakes, or ensuring data lineage and reproducibility in biological research. It covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integration with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
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Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially for cross-database analysis and identifier mapping.
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Generate Meta-analysis funnel plots and perform publication bias testing. Takes CSV file with Meta-analysis data as input, outputs funnel plot PNG, Egger test and Begg test results.
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Digital pathology image processing toolkit for whole slide images (WSI). Supports WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.
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Machine learning toolkit for genomic interval (BED) data; use it when you need to tokenize BED collections and train embeddings for regions/cells/labels, build consensus peak universes, or run similarity search and downstream ML on chromatin accessibility datasets.
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Screen full-text papers against inclusion/exclusion criteria, with optional PubMed metadata check using PMID. Use when the user needs to evaluate a paper for a meta-analysis.
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Screens research papers based on title/abstract and inclusion criteria, providing a structured Yes/No/Maybe decision. Use when you need to filter literature for meta-analysis or systematic reviews.
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Draw ROB2 risk-of-bias plots, including a Traffic Light Plot and a Summary Bar Plot. Input is a CSV file with ROB2 assessments for each study; output are two PNG plot files.
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Generate forest plots for meta-analysis of survival data. Input is a CSV file containing study names, HR and 95% confidence intervals, output forest plot PNG and data table CSV. Supports both R and Python scripts.
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Analyzes the feasibility of a proposed Meta-analysis topic by searching for existing Meta-analyses and Clinical Trials on PubMed/ClinicalTrials.gov. Use when you need to evaluate if a topic is viable for a new Meta-analysis.
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Constraint-based reconstruction and analysis (COBRA) for metabolic models; use when you need to simulate growth/production, analyze flux ranges, or run knockout and medium studies from SBML/JSON/YAML models.
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Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
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Statistical analysis and reporting for experimental datasets; use when you need to interpret experimental results, test significance (t-tests/ANOVA), or generate reproducible reports.
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A low-level plotting library for comprehensive customization. Use when fine-grained control over every plot element is needed, creating new types of charts, or integrating into specific scientific workflows. Can export to PNG/PDF/SVG for publication. For quick statistical charts, use seaborn; for interactive charts, use plotly; for journal-style, publication-ready multi-panel charts, use scientific-visualization.
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DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.
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Generate Circos configuration files for circular genomics data visualization. Supports genomic variations (SNPs, CNVs, structural variants), cell-cell communication networks, and custom track configurations for publication-ready circular plots.
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Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows.
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Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.
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Clinical Research Bias Assessment - Case-Control Study (NOS) v2.3.0. Use when you need to assess the bias of a case-control study using the Newcastle-Ottawa Scale (NOS) criteria, or when evaluating the quality of a medical paper.
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Use facs gating viz style for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
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Filter compound libraries based on Lipinski's Rule of Five for drug-likeness.
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Use when cleaning clinical trial data, preparing data for FDA/EMA submission, standardizing SDTM datasets, handling missing values in clinical studies, detecting outliers in lab results, or converting raw CRF data to CDISC format. Cleans and standardizes clinical trial data fo...
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Generate meta-analysis forest plots for binary classification data. Input is a CSV file containing study names, event counts and sample sizes for experimental and control groups. Output includes forest plot PNG and data table CSV.
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