데이터 분석, 머신러닝, LLM 앱, 프롬프트 설계 (9.1천건)
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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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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Evaluates the quality of cohort studies using the Newcastle-Ottawa Scale (NOS). Use when the user provides a cohort study article or text and needs a quality assessment report.
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Use when refactoring research code for publication, adding documentation to existing analysis scripts, creating reproducible computational workflows, or preparing code for sharing with collaborators. Transforms research code into publication-ready, reproducible workflows. Adds documentation, implements error handling, creates environment specifications, and ensures computational reproducibility for scientific publications.
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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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A Python library for reading, writing, and analyzing geospatial vector data; use it when you need spatial operations (buffer/overlay/join), CRS reprojection, or map visualization on formats like Shapefile/GeoJSON/GeoPackage or PostGIS.
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Perform quantitative meta-analysis with effect size calculation, forest plots, funnel plots, and heterogeneity assessment. Use when: user asks to combine results from multiple studies, calculate pooled effect sizes, assess publication bias, or create forest/funnel plots. NOT f...
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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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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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Generate leave-one-out sensitivity analysis plots for meta-analysis. Input is a CSV file containing meta-analysis data; outputs are a sensitivity forest plot (PNG) and a sensitivity data table (CSV) showing pooled effect estimates after excluding each study in turn.
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ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.
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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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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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Performs epidemiological analyses including disease modeling (SIR/SEIR), outbreak investigation, risk factor identification, incidence/prevalence estimation, and causal inference from observational data; trigger when users discuss disease spread, public health data, or populat...
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Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.
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Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.
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A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.
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Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instrum...
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Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular...
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Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O, lightweight sequence manipulation, or scalable processing of large sequence datasets.
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Extracts clinical trial baseline data (study, region, participants, etc.) from article text or PMID. Checks PubMed for metadata; always falls back to LLM extraction for full details.
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Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.
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Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX.
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Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.
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