Daily repo health check — scans recent commits, CI failures, dependency drift, performance regressions, and untested code paths.
An LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design. — from bg-szy/TOP-SKILLS
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival cu — from…
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignmen — from…
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, gener — from…
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping — from…
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy.
Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA e — from…
Compute RDKit-driven molecular properties (MW, logP, TPSA, QED, Lipinski) for a SMILES string to support downstream drug discovery tools.
Calculates and harmonizes Tumor Mutational Burden (TMB) across platforms to predict immunotherapy response.
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLI — from…
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython.
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, or — from…
Defense-in-depth security validation — multi-layered checks for OWASP Top 10, secrets, auth, crypto, and data protection.
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with M — from…
Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes.
Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib. Use when creating publication-quality tree figures, customizing colors and labels, or exporting to…
Database performance audit — detects N+1 queries, missing indexes, join opportunities, slow queries, EXPLAIN analysis, and per-endpoint DB call counts.
Download large datasets from NCBI efficiently using history server, batching, and rate limiting. Use when performing bulk sequence downloads, handling large query results — from…
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCa — from…
Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions.
Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.
Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position.
AI-powered virtual laboratory orchestrating multi-agent scientific research teams for autonomous hypothesis generation, experimental design, and validation in biomedical research.
Calculates statistical power and minimum sample sizes for RNA-seq, ATAC-seq, and other sequencing experiments.
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any se — from…
Create metagene plots and browser tracks for RNA modification data. Use when visualizing m6A distribution patterns around genomic features like stop codons.
De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly…
Reference for building Starknet applications using starknet.js v9.x SDK, including contract interaction, account management, transaction handling, fee estimation, wallet — from…
AI-powered minimal residual disease (MRD) analysis for multiple myeloma using next-generation flow cytometry, NGS, and mass spectrometry approaches.
Analyzes longitudinal wearable sensor data (heart rate, activity, sleep) to detect anomalies and provide personalized health insights.
Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data.
Detect positive selection using dN/dS (omega) tests with PAML codeml and HyPhy. Identify sites and branches under adaptive evolution through codon models and branch-site tests.
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or in — from…
An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion). — from bg-szy/TOP-SKILLS
Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks.
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statis — from…
AI-powered spatial integration of multi-omics datasets using probabilistic alignment for comprehensive tissue atlas construction and cellular state mapping.
Lightweight web fuzzing via ffuf — directory discovery, parameter testing, subdomain enumeration.
Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines.
Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution.
Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome.
Call protein-RNA binding site peaks from CLIP-seq data using CLIPper, PureCLIP, or Piranha. Use when identifying RBP binding sites from aligned CLIP reads. — from bg-szy/TOP-SKILLS
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical sig — from…
Multi-omic biomarker discovery studio that ingests expression + metadata, performs QC, multi-strategy feature selection, nested CV model training, survival analysis hooks, and…
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building anno — from…
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery.
End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation. — from bg-szy/TOP-SKILLS
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into…
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or — from…
An agent that interprets spatial transcriptomics data to propose mechanistic hypotheses and analyze tissue organization.
End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visual — from…
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.
AI-powered spatial epigenomics analysis combining chromatin accessibility, histone modifications, and DNA methylation with spatial coordinates for tissue architecture mapping.
Automates the drafting of regulatory documents (e.g., FDA CTD sections) with citation management and audit trails.
AI-powered analysis of patient-derived organoid (PDO) drug screening for personalized oncology treatment selection and biomarker discovery.
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profi — from…