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14810 skills availablebio-clip-seq-binding-site-annotation
library(ChIPseeker) library(TxDb.Hsapiens.UCSC.hg38.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene peaks <- readPe...
writing-plans
Write comprehensive implementation plans assuming the engineer has zero context for our codebase and questionable taste....
transformers
The Hugging Face Transformers library provides access to thousands of pre-trained models for tasks across NLP, computer ...
simo-multiomics-integration-agent
The SIMO Multiomics Integration Agent performs spatial integration of multi-omics datasets through probabilistic alignme...
biomedical-search
Search across all major biomedical databases (PubMed, bioRxiv, medRxiv, ClinicalTrials.gov, FDA drug labels) simultaneou...
bio-epitranscriptomics-m6anet-analysis
Documentation: https://m6anet.readthedocs.io/ guppybasecaller \ -i fast5dir \ -s basecalled \ --flowcell FLO-MIN106 \ --...
citation-management
Manage citations systematically throughout the research and writing process. This skill provides tools and strategies fo...
time-stepping
Provide a reliable workflow for choosing, ramping, and monitoring time steps plus output/checkpoint cadence. Python 3.8+...
vcf-manipulation
Merge, concat, sort, and compare VCF files using bcftools. | Operation | Command | Use Case | |-----------|---------|---...
bio-hi-c-analysis-loop-calling
Reference examples tested with: bedtools 2.31+, cooler 0.9+, cooltools 0.6+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, ...
lit-synthesizer
You are the Lit Synthesizer, a specialised agent for biomedical literature search and synthesis. PubMed Search: Query NC...
benchling-integration
Benchling is a cloud platform for life sciences R&D. Access registry entities (DNA, proteins), inventory, electronic lab...
infographics
Infographics are visual representations of information, data, or knowledge designed to present complex content quickly a...
single-clustering
This skill distills the single-cell tutorials tcluster.ipynb and tsinglebatch.ipynb. Use it when a user wants to preproc...
bio-workflows-merip-pipeline
FASTQ → QC → Align IP+Input → Peak calling → Annotation → Differential → Visualization fastp -i IPR1.fq.gz -I IPR2.fq.gz...
pytorch-lightning
PyTorch Lightning is a deep learning framework that organizes PyTorch code to eliminate boilerplate while maintaining fu...
bio-spatial-transcriptomics-spatial-statistics
Reference examples tested with: numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+, squidpy 1.3+ Before using code patt...
chromosomal-instability-agent
The Chromosomal Instability Agent analyzes CIN signatures to predict cancer prognosis, immunotherapy response, and thera...
gene-panel-design-agent
The Gene Panel Design Agent provides AI-driven design of targeted sequencing panels for clinical diagnostics, cancer pro...
bio-genome-engineering-grna-design
Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions...
bio-reporting-jupyter-reports
import papermill as pm pm.executenotebook( 'analysistemplate.ipynb', 'outputreport.ipynb', parameters={ 'inputfile': 'da...
cellfree-rna-agent
The Cell-Free RNA Analysis Agent provides comprehensive analysis of circulating cell-free RNA (cfRNA) from plasma and ot...
bio-flow-cytometry-differential-analysis
Reference examples tested with: R stats (base), edgeR 4.0+, ggplot2 3.5+, limma 3.58+ Before using code patterns, verify...
organoid-drug-response-agent
The Organoid Drug Response Agent provides AI-driven analysis of patient-derived organoid (PDO) drug screening data for p...