Use when you have extracted quantitative genomic features (e.g., insulation scores, boundary annotations) as a pandas DataFrame with bin coordinates and boolean or numeric…
Use when after computing per-bin coverage depth using cooltools.coverage() on a loaded cooler object, when you need to (1) share the coverage track with non-Python tools, (2)…
Use when you have aligned ChIP-Seq reads (in BED or BEDPE format) and need to convert them into quantitative genome-wide signal tracks (coverage, p-value, or q-value scores) for…
Use when you have generated or received bedGraph files from paired-end sequencing (via bedtools genomecov or similar) and need to verify they conform to UCSC bedGraph format…
Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features.
Plaited behavioral programming patterns for event-driven coordination and symbolic reasoning. Use when implementing behavioral programs with behavioral()/useBehavioral, designing…
Biological foundations of behavior and mental processes. Covers brain structure and function (cerebral cortex, limbic system, brainstem, cerebellum, lateralization),…
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data m — from…
Score deep research agents on benchmark tasks using factual verification, report-quality scoring, and process evaluation before model or workflow changes ship.
Audit an ML benchmark for data leakage with karyon — measure how much a reported accuracy is inflated by train/test contamination.
[METHODOLOGY] Industry benchmark research — reverse-engineer how the fastest-growing companies in a given industry actually scaled (source harvest → company synthesis →…
Audit government benefits and entitlement systems for fraud prevention, detection, and recovery capabilities.
Query the KBase BERDL (BER Data Lakehouse) databases. Use when the user asks to explore pangenome data, query species information, get genome statistics, analyze gene clusters,…
Get started with the BERIL Research Observatory. Use when a user is new, wants orientation, or asks what they can do.
Use this agent when you need to research external best practices, documentation, and examples for any technology or development practice.
Optimal posting time analysis — research platform-specific engagement patterns for the user's niche and audience, recommend best times to post on note, X, and Instagram.
🧠 Classify an incoming task by its shape (decision, diagnosis, research, creative, communication, learning, negotiation) and its stakes, then select which skills to deploy at what…
Use when you have assembled genome sequences (contigs or scaffolds in FASTA format) and want to identify putative BGCs and their precursor peptides before constructing a RiPP…
Use when you have computed raw strain correlation scores and IOKR scores for the same set of GCF–MF (gene cluster family–molecular feature) pairs, and you want to compare or…
Use when you have: (1) a trained IOKR model mapping from spectrum kernels to molecular fingerprints, (2) MS2 spectra from your sample, (3) a set of candidate BGCs with known or…
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.
Evidence-based medical knowledge and research mentor grounded in the Bian Que tradition. Covers clinical reasoning, diagnostic thinking (望闻问切), pharmacology, pathology,…
Use before any research activity or significant decision. Reviews cognitive biases relevant to the current stage.
Use when after computeDeviations has generated a SummarizedExperiment object with z-score assays reflecting bias-corrected deviations of observed vs.
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC — from…
Use when you have executed a binary classifier (such as BitterPredict.m) on a set of molecules with chemical structure descriptors and need to translate the raw predictions into a…
Use when you have a pre-trained TCN spectrum encoder, annotated MS/MS spectra paired with ground-truth molecular formulas, and you want to train only the formula ranking and…
Use when when setting up a bioinformatics pipeline (particularly Hi-C data processing) that depends on multiple external binaries with version constraints, and you need to…
Use when you need to run a binary, trace execution, or observe runtime behavior. Runtime analysis via QEMU emulation, GDB debugging, and Frida hooking - syscall tracing ( — from…
Use when analyzing binary structure, disassembling code, or decompiling functions. Deep static analysis via radare2 (r2) and Ghidra headless - function enumeration, cross — from…
Use when ready to document findings, generate a report, or summarize binary analysis results. Compiles analysis findings into structured reports - correlates facts from t — from…
Use when reverse engineering tools are missing, not working, or need configuration. Installation guides for radare2 (r2), Ghidra, GDB, QEMU, Frida, binutils, and cross-co — from…
Use when first encountering an unknown binary, ELF file, executable, or firmware blob. Fast fingerprinting via rabin2 - architecture detection (ARM, x86, MIPS), ABI ident — from…
Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting…
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics.
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics.
Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way.
Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.
Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program…
Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro).
Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate,…
Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-fa — from…
Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes.
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package.
Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or…
Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR.
Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments.
Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data.
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples.
Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or…
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions.
Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective…
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discove — from…
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks.
Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R…
Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cu — from…
Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data bo — from…
Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated…
Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE)…
Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood,…