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14810 skills availablebio-population-genetics-plink-basics
File formats, conversion, and quality control filtering with PLINK 1.9 and 2.0. | File | Contents | |------|----------| ...
bio-phylo-distance-calculations
Compute distances from alignments and construct phylogenetic trees. from Bio import Phylo, AlignIO from Bio.Phylo.TreeCo...
bio-expression-matrix-sparse-handling
import numpy as np def checksparsity(counts): zeros = (counts == 0).sum().sum() total = counts.size sparsity = zeros / t...
structural-variant-calling
configManta.py \ --bam sample.bam \ --referenceFasta reference.fa \ --runDir mantarun mantarun/runWorkflow.py -j 8 confi...
spatial-proteomics
import scimap as sm import anndata as ad adata = ad.readh5ad('spatialproteomics.h5ad') sm.pp.log1p(adata) sm.pp.rescale(...
tooluniverse-cancer-variant-interpretation
Comprehensive clinical interpretation of somatic mutations in cancer. Transforms a gene + variant input into an actionab...
histolab
Histolab is a Python library for processing whole slide images (WSI) in digital pathology. It automates tissue detection...
bio-spatial-transcriptomics-image-analysis
Reference examples tested with: Cellpose 3.0+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scikit-learn 1.4...
hrv-alexithymia-expert
You are an expert in Heart Rate Variability (HRV) biometrics and Alexithymia (emotional awareness difficulties), special...
bio-restriction-fragment-analysis
from Bio import SeqIO from Bio.Restriction import EcoRI record = SeqIO.read('sequence.fasta', 'fasta') seq = record.seq ...
ctdna-dynamics-mrd-agent
The ctDNA Dynamics MRD Agent provides comprehensive analysis of circulating tumor DNA dynamics for molecular residual di...
bio-workflows-smrna-pipeline
FASTQ → cutadapt trim → miRDeep2 → Quantification → DESeq2 → Target prediction cutadapt -a TGGAATTCTCGGGTGCCAAGG \ --min...
bio-pdb-structure-io
Reference examples tested with: BioPython 1.83+, scanpy 1.10+ Before using code patterns, verify installed versions matc...
bulk-stringdb-ppi
Invoke this skill when the user has a list of genes and wants to explore STRING protein–protein interactions via omicver...
radgpt-radiology-reporter
An LLM-based agent designed to summarize and explain complex radiology reports for patients and clinicians. Patient Comm...
bio-microbiome-amplicon-processing
Reference examples tested with: DADA2 1.30+, cutadapt 4.4+ Before using code patterns, verify installed versions match. ...
tooluniverse-statistical-modeling
Comprehensive statistical modeling skill for fitting regression models, survival models, and mixed-effects models to bio...
neurokit2
NeuroKit2 is a comprehensive Python toolkit for processing and analyzing physiological signals (biosignals). Use this sk...
bio-machine-learning-model-validation
Simple train/test splits overestimate performance on small omics datasets. Nested CV provides unbiased estimates by sepa...
rdkit
RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This ski...
tme-immune-profiling-agent
The TME Immune Profiling Agent provides comprehensive tumor microenvironment (TME) immune profiling by integrating multi...
vcf-annotator
You are the VCF Annotator, a specialised agent for variant annotation and interpretation. VEP Annotation: Run Ensembl Va...
bio-variant-calling-deepvariant
Reference examples tested with: GATK 4.5+, bcftools 1.19+ Before using code patterns, verify installed versions match. I...
bio-imaging-mass-cytometry-phenotyping
Reference examples tested with: FlowSOM 2.10+, anndata 0.10+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, s...