Tools
Local RAG for document ingestion and querying
This comprehensive local RAG pipeline enables the ingestion of various file types, supporting both raw data and complex visual PDF content. It executes advanced hybrid searches, providing semantic and keyword results, and includes context e…
Advanced OOXML Editing for Word Documents
This tool provides granular control over the underlying OOXML structure of .docx files, enabling complex edits such as adding comments, managing footnotes, or performing bulk replacements. It ensures all modifications are correctly marked a…
Advanced OOXML Word Document Manipulation Tool
This tool provides granular control over the OOXML structure of Word documents, enabling complex operations such as creating from markdown, managing tracked changes, and auditing structural integrity. It allows developers to programmaticall…
Agent Dispute Resolution and Judging Tool
This tool acts as a neutral arbiter, evaluating disputes between agents by strictly comparing a deliverable against a binding job specification. It outputs a structured JSON ruling, determining if the deliverer wins, the customer wins, or i…
Comprehensive AI Data and Model Quality Evaluator
Dingo provides a comprehensive framework for evaluating data and AI outputs using both deterministic rule-based checks and advanced LLM-based metrics. It supports complex workflows, including RAG evaluation and autonomous fact-checking, via…
Decompose text into structured semantic units
This tool deterministically parses raw text or URLs into structured semantic units, classifying elements by authority, risk, and attention score. It is ideal for pre-processing complex documents like specifications or contracts, significant…
Figma automation via CLI and JSX
A command-line interface for programmatic Figma manipulation using imperative commands or declarative JSX rendering. It enables the automated creation of frames, components, and styles, with support for Iconify integration and Storybook exp…
Comprehensive X (Twitter) API Integration Tool
This tool provides comprehensive access to X (Twitter) data, enabling advanced read, write, and extraction operations via a dedicated API key. It supports complex workflows such as user lookups, bulk media downloading, monitoring, and posti…
Manage LinkedIn publishing and engagement via API
This tool suite facilitates comprehensive LinkedIn interaction, allowing users to publish posts, comment on existing content, and react to updates. It requires Unipile credentials and enforces a safe workflow by defaulting to dry-run mode, …
Persistent Memory and Knowledge Graph for Agents
This system provides persistent, structured memory for agents, allowing them to store, recall, and connect context across sessions. It utilizes a hybrid search mechanism combining vector, BM25, and graph traversal for robust knowledge compo…
Multi-Platform Social Media Content Scheduler
This tool facilitates the creation, scheduling, and management of content across numerous social media platforms, including Facebook, Instagram, X, and LinkedIn. It supports batch posting, media uploads, and detailed platform-specific contr…
Comprehensive Biomedical Data Retrieval and Analysis Tool
This CLI tool provides structured, multi-hop access to vast biomedical knowledge, enabling developers to query genes, drugs, diseases, and variants across multiple domains. It supports complex workflows for tasks such as adverse event check…
Query Genomic Annotations from UCSC Browser API
This tool provides programmatic access to the UCSC Genome Browser REST API, enabling the retrieval of comprehensive, cross-experiment genomic annotations. Developers can query regulatory elements, TF binding clusters, and DNA sequences for …
AI-First CMS for Structured Content Management
Contentrain is a Git-based, AI-first CMS designed for managing structured content using defined models. It provides a robust set of MCP tools for scaffolding, validation, and merging content across various formats, ensuring deterministic co…
CUT/CUT Peak Calling Pipeline
This tool executes a comprehensive Nextflow pipeline for processing CUT or CUT FASTQ data. It handles alignment, spike-in normalization, and generates peak calls using SEACR or MACS2, producing normalized signal tracks and genomic peaks.
Aggregate Hi-C Chromatin Loop Catalogs
This tool facilitates the construction of comprehensive chromatin loop catalogs by merging paired-end Hi-C loop calls (BEDPE) from disparate ENCODE experiments. It manages critical steps such as resolution harmonization, quality filtering, …
Annotate regulatory variants with population genetics
This tool facilitates the annotation of ENCODE regulatory variants by querying gnomAD for population allele frequencies and gene constraint scores (pLI, LOEUF). It enables developers to prioritize variants by assessing rarity and functional…
Real-time collaboration rooms for AI agents
This tool provides a structured interface for AI agents to interact within a real-time, multi-agent collaboration environment. Agents can join rooms, send broadcast or direct messages, and manage message history and room metadata for coordi…
Ensembl API for Variant and Gene Annotation
This tool interfaces with the Ensembl REST API to perform comprehensive genomic annotations, including variant consequence prediction (VEP), regulatory feature overlap, and coordinate liftover between assemblies. It also facilitates gene ID…
Persistent Memory for AI Coding Agents
Provides a persistent memory layer for AI coding agents, enabling semantic search, task checkpointing, and cross-session context retention. It operates locally using CPU-only embeddings and integrates with MCP-compatible clients.
Deconvolve Bulk Genomics with Single-Cell Context
This tool provides programmatic access to the CellxGene Census, enabling developers to bridge bulk ENCODE functional genomics data with cell-type-specific expression profiles. It allows for the deconvolution of broad regulatory signals by q…
Persistent memory for AI coding agents
This tool provides persistent, queryable memory for AI agents, allowing them to store critical decisions, user preferences, and lessons learned. It uses a hybrid retrieval architecture (vector similarity and full-text search) to ensure agen…
Systematic ENCODE Batch Analysis and QC Toolkit
This tool facilitates systematic, large-scale batch operations across multiple ENCODE experiments. It guides users through quality control screening, comparison table generation, and bulk data downloading using established ENCODE metrics an…
Query UCSC Genome Browser REST API
Programmatically access the UCSC Genome Browser REST API to retrieve comprehensive genomic data, including cCRE annotations, TF binding clusters, and DNA sequences for any specified locus. This tool facilitates cross-referencing ENCODE data…