Processing
Data transformation and parsing
tooluniverse-immune-repertoire-analysis
by mims-harvard
Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3 characteristics, convergence, and predict epitope specificity. Integrate with single-cell data for clonotype-phenotype associations. Use for adaptive immune response profiling, cancer immunotherapy research, vaccine response assessment, autoimmune disease studies, or repertoire diversity analysis in immunology research.
tooluniverse-pharmacovigilance
by mims-harvard
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pharmacogenomic risk variants. Use when asked about drug safety, adverse events, post-market surveillance, or risk-benefit assessment.
tooluniverse-polygenic-risk-score
by mims-harvard
Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles, interprets PRS percentiles, and assesses disease predisposition across conditions including type 2 diabetes, coronary artery disease, and Alzheimer's disease. Use when asked to calculate polygenic risk scores, interpret genetic risk for complex diseases, build custom PRS from GWAS data, or answer questions like "What is my genetic predisposition to breast cancer?"
devtu-create-tool
by mims-harvard
Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniverse, implement new API integrations, create tool wrappers for scientific databases/services, expand ToolUniverse capabilities, or follow ToolUniverse contribution guidelines. Supports creating tool classes, JSON configurations, validation, error handling, and test examples.
tooluniverse-gwas-study-explorer
by mims-harvard
Compare GWAS studies, perform meta-analyses, and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog and Open Targets Genetics to compare study designs, effect sizes, ancestry diversity, and heterogeneity statistics. Use when comparing GWAS studies for a trait, performing meta-analysis of genetic loci, assessing replication across cohorts, or exploring the genetic architecture of complex diseases.
tooluniverse-epigenomics
by mims-harvard
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility, multi-omics integration (expression + methylation correlation), and genome-wide statistics. Pure Python computation (pandas, scipy, numpy, pysam, statsmodels) plus ToolUniverse annotation tools (Ensembl, ENCODE, SCREEN, JASPAR, ReMap, RegulomeDB, ChIPAtlas). Supports BED, BigWig, methylation beta-value matrices, Illumina manifest files, and multi-sample clinical data. Use when processing methylation data, ChIP-seq peaks, ATAC-seq signals, or answering questions about CpG sites, differential methylation, chromatin accessibility, histone marks, or epigenomic statistics.
design-taste-frontend
by Leonxlnx
Senior UI/UX Engineer. Architect digital interfaces overriding default LLM biases. Enforces metric-based rules, strict component architecture, CSS hardware acceleration, and balanced design engineering.
analyzing-typosquatting-domains-with-dnstwist
by mukul975
Detect typosquatting, homograph phishing, and brand impersonation domains using dnstwist to generate domain permutations and identify registered lookalike domains targeting your organization.
analyzing-slack-space-and-file-system-artifacts
by mukul975
Examine file system slack space, MFT entries, USN journal, and alternate data streams to recover hidden data and reconstruct file activity on NTFS volumes.
coding-standards
by affaan-m
Universal coding standards, best practices, and patterns for TypeScript, JavaScript, React, and Node.js development.
analyzing-malware-family-relationships-with-malpedia
by mukul975
Use the Malpedia platform and API to research malware family relationships, track variant evolution, link families to threat actors, and integrate YARA rules for detection across malware lineages.
analyzing-lnk-file-and-jump-list-artifacts
by mukul975
Analyze Windows LNK shortcut files and Jump List artifacts to establish evidence of file access, program execution, and user activity using LECmd, JLECmd, and manual binary parsing of the Shell Link Binary format.
analyzing-pdf-malware-with-pdfid
by mukul975
Analyzes malicious PDF files using PDFiD, pdf-parser, and peepdf to identify embedded JavaScript, shellcode, exploits, and suspicious objects without opening the document. Determines the attack vector and extracts embedded payloads for further analysis. Activates for requests involving PDF malware analysis, malicious document analysis, PDF exploit investigation, or suspicious attachment triage.
analyzing-active-directory-acl-abuse
by mukul975
Detect dangerous ACL misconfigurations in Active Directory using ldap3 to identify GenericAll, WriteDACL, and
analyzing-malware-sandbox-evasion-techniques
by mukul975
Detect sandbox evasion techniques in malware samples by analyzing timing checks, VM artifact queries, user interaction
agent-sort
by affaan-m
Build an evidence-backed ECC install plan for a specific repo by sorting skills, commands, rules, hooks, and extras into DAILY vs LIBRARY buckets using parallel repo-aware review passes. Use when ECC should be trimmed to what a project actually needs instead of loading the full bundle.
analyzing-memory-forensics-with-lime-and-volatility
by mukul975
'Performs Linux memory acquisition using LiME (Linux Memory Extractor) kernel module and analysis with Volatility
analyzing-network-flow-data-with-netflow
by mukul975
Parse NetFlow v9 and IPFIX records to detect volumetric anomalies, port scanning, data exfiltration, and C2 beaconing
analyzing-malicious-pdf-with-peepdf
by mukul975
Perform static analysis of malicious PDF documents using peepdf, pdfid, and pdf-parser to extract embedded JavaScript,
analyzing-network-traffic-with-wireshark
by mukul975
'Captures and analyzes network packet data using Wireshark and tshark to identify malicious traffic patterns,
analyzing-network-packets-with-scapy
by mukul975
Craft, send, sniff, and dissect network packets using Scapy for protocol analysis, network reconnaissance, and
cpp-coding-standards
by affaan-m
C++ coding standards based on the C++ Core Guidelines (isocpp.github.io). Use when writing, reviewing, or refactoring C++ code to enforce modern, safe, and idiomatic practices.
analyzing-kubernetes-audit-logs
by mukul975
'Parses Kubernetes API server audit logs (JSON lines) to detect exec-into-pod, secret access, RBAC modifications,
analyzing-cloud-storage-access-patterns
by mukul975
Detect abnormal access patterns in AWS S3, GCS, and Azure Blob Storage by analyzing CloudTrail Data Events, GCS