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Topic: skills

17,247 skills in this topic.

bio-crispr-screens-base-editing-analysis Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies. Use when quantifying CRISPR base editor results, comparing ABE vs CBE efficiency, or assessing prime editing fidelity.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
alphafold Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-proteomics-peptide-identification Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-entrez-search
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-expression-matrix-gene-id-mapping
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-longitudinal-monitoring 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 detecting molecular relapse before clinical progression.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-metagenomics-metaphlan 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 HMP/other MetaPhlAn studies.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-population-genetics-linkage-disequilibrium
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-multi-omics-mixomics-analysis 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 between groups.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-geo-data
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-chipseq-motif-analysis De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-read-qc-umi-processing Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-multi-omics-similarity-network 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 networks.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-pathway-enrichment-visualization 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.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
adaptyv Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-methylation-calling 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.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-crispr-screens-hit-calling Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen count data after QC passes.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-epitranscriptomics-merip-preprocessing
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-atac-seq-atac-qc Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-clinical-databases-hla-typing Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-clip-seq-clip-preprocessing
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-crispr-screens-batch-correction Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-genome-intervals-coverage-analysis
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-clinical-databases-polygenic-risk Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009