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numerical-integration
Provide a reliable workflow to select integrators, set tolerances, and manage adaptive time stepping for time-dependent simulations. Python 3.8+ NumPy...
bio-variant-normalization
Reference examples tested with: bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pack...
bio-phylo-tree-manipulation
Modify phylogenetic tree structure: rooting, pruning, ladderizing, and subtree extraction. from Bio import Phylo from io import StringIO tree = Phylo....
bio-workflow-management-cwl-workflows
cwlVersion: v1.2 class: CommandLineTool baseCommand: fastqc inputs: fastq: type: File inputBinding: position: 1 outputs: html: type: File outputBindin...
single-preprocessing
Follow this skill when a user needs to reproduce the preprocessing workflow from the omicverse notebooks tpreprocess.ipynb, tpreprocesscpu.ipynb, and ...
uspto-database
USPTO provides specialized APIs for patent and trademark data. Search patents by keywords/inventors/assignees, retrieve examination history via PEDS, ...
paper-2-web
This skill enables the transformation of academic papers into multiple promotional and presentation formats using the Paper2All autonomous pipeline. T...
bio-orchestrator
You are the Bio Orchestrator, a ClawBio meta-agent for bioinformatics analysis. Your role is to: Understand the user's biological question and determi...
bio-single-cell-markers-annotation
Reference examples tested with: DESeq2 1.42+, pandas 2.2+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions diffe...
tcr-repertoire-analysis-agent
The TCR Repertoire Analysis Agent provides comprehensive T-cell receptor repertoire analysis for cancer immunology applications. It leverages deep lea...
bio-flow-cytometry-clustering-phenotyping
Reference examples tested with: FlowSOM 2.10+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: R: packag...
bio-ctdna-mutation-detection
Reference examples tested with: Ensembl VEP 111+, SnpEff 5.2+, VarDict 1.8+, pandas 2.2+, pysam 0.22+ Before using code patterns, verify installed ver...