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このリポジトリの skills
SkillsMP は FreedomIntelligence/OpenClaw-Medical-Skills から 465 件の skill を収集しています。skill を開くとソースと詳細を確認できます。
FreedomIntelligence/OpenClaw-Medical-Skills収集済み skill 465 件中 40 件を表示しています。
Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction trends, mutation clearance kinetics, and defines molecular response criteria. Use when monitoring patients during therapy or…
原文の言語: 英語
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.
原文の言語: 英語
Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.
原文の言語: 英語
Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio run quality or filtering reads before assembly…
原文の言語: 英語
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.
原文の言語: 英語
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classes, chain composition, or lipid-specific pathways.
原文の言語: 英語
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.
原文の言語: 英語
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessing.
原文の言語: 英語
Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use when correcting technical variation in metabolomics data before statistical analysis.
原文の言語: 英語
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.
原文の言語: 英語
Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery. Use when identifying differentially abundant metabolites or building classification models.
原文の言語: 英語
Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use when quantifying specific metabolites using calibration curves and internal standards.
原文の言語: 英語
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.
原文の言語: 英語
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.
原文の言語: 英語
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.
原文の言語: 英語
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
原文の言語: 英語
Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.
原文の言語: 英語
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with…
原文の言語: 英語
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain…
原文の言語: 英語
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic…
原文の言語: 英語
Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific methylation signatures and performs tissue-of-origin deconvolution. Use when using methylation biomarkers for…
原文の言語: 英語
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
原文の言語: 英語
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis.
原文の言語: 英語
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types.
原文の言語: 英語
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR…
原文の言語: 英語
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplicon FASTQ files to generate an ASV table for…
原文の言語: 英語
Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.
原文の言語: 英語
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome…
原文の言語: 英語
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.
原文の言語: 英語
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.
原文の言語: 英語
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.
原文の言語: 英語
Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by…
原文の言語: 英語
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use…
原文の言語: 英語
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types. Use when preparing multi-omics datasets for integration analysis.
原文の言語: 英語
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis. Use when performing supervised multi-omics integration or identifying features that discriminate…
原文の言語: 英語
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation. Use when integrating RNA-seq, proteomics, methylation, or other omics to discover latent factors driving…
原文の言語: 英語
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network. Use when performing patient stratification or integrating multi-omics data into unified similarity…
原文の言語: 英語
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
原文の言語: 英語
Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.
原文の言語: 英語
Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot.
原文の言語: 英語