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DeepTools NGS Analysis Toolkit

K-Dense-AI/scientific-agent-skills

A comprehensive Python command-line toolkit for processing and visualizing high-throughput sequencing data including ChIP-seq, RNA-seq, and ATAC-seq. Performs quality control, normalization, sample comparison, and generates publication-quality genomic visualizations with bigWig conversion and heatmap profiles.

Neuropixels Neural Data Analysis

neuropixels-analysis

K-Dense-AI/scientific-agent-skills

End-to-end analysis toolkit for Neuropixels extracellular recordings using SpikeInterface. Supports loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift correction, spike sorting with Kilosort4 and other algorithms, quality metrics computation, and AI-assisted unit curation for publication-ready neural data analysis.

PathML Computational Pathology Workflows

K-Dense-AI/scientific-agent-skills

Build local, research-only computational pathology workflows with PathML: load and tile whole-slide images, run preprocessing and QC pipelines, manage h5path data, quantify multiplex images, construct spatial graphs, and plan bounded model inference.

Polars DataFrame Analytics

K-Dense-AI/scientific-agent-skills

High-performance Python DataFrame library built on Apache Arrow. Covers expression-based API, lazy query optimization, streaming out-of-core processing, aggregations, window functions, joins, and pandas migration for ETL and analytics pipelines.

Python Genomic File Processing

K-Dense-AI/scientific-agent-skills

A Python library for reading, querying, filtering, and writing genomic file formats including SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, and tabix data. Supports pileup, coverage analysis, indexing, and CRAM reference operations with HTSlib integration. Ideal for bioinformatics workflows requiring low-level streaming access to genomic data.

Vaex Large Dataset Analysis

K-Dense-AI/scientific-agent-skills

Vaex is a high-performance Python library designed for processing and analyzing large tabular datasets that exceed available RAM. It supports out-of-core DataFrame operations, lazy evaluation, fast aggregations, and efficient visualization of big data. Ideal for working with massive CSV, HDF5, Arrow, or Parquet files, performing statistics on billions of rows, and building machine learning pipelines without memory constraints.

Anthropic Event Streaming And Batch Processing

anth-webhooks-events

jeremylongshore/claude-code-plugins-plus-skills

This guide teaches developers how to implement robust, event-driven architecture patterns with the Anthropic Claude API. It covers two key methods: Server-Sent Events (SSE) for real-time streaming responses, and the Message Batches API for high-volume, asynchronous bulk processing. Use this when building real-time chat features or processing large datasets offline.

Apify Core Storage and Workflow Management

apify-core-workflow-b

jeremylongshore/claude-code-plugins-plus-skills

Provides comprehensive programmatic control over Apify's core data infrastructure, including Datasets, Key-Value Stores, and Request Queues. This skill allows users to perform CRUD operations on various storage types, manage data persistence, and orchestrate complex, multi-stage data pipelines (e.g., scrape -> transform -> export). Ideal for building robust, end-to-end web scraping and data processing automation workflows.

Clari API Rate Limit Handling and Scheduling

clari-rate-limits

jeremylongshore/claude-code-plugins-plus-skills

This skill provides robust mechanisms to interact with the Clari API, specifically designed to handle rate limiting (HTTP 429 errors) and manage asynchronous bulk export jobs. It implements exponential backoff and sequential scheduling, ensuring reliable data retrieval and forecasting exports without hitting API limits. Ideal for automated data pipelines and background job processing.

Fathom AI Meeting Integration Deployment

fathom-deploy-integration

jeremylongshore/claude-code-plugins-plus-skills

This skill provides a comprehensive guide and implementation for deploying a containerized Fathom AI meeting service. It is designed to handle the processing of meeting transcripts, summaries, and action items via webhooks. The solution includes Docker setup, environment variable management, robust health checks, and detailed steps for implementing rolling updates, ensuring continuous and reliable meeting data synchronization.

Local Fathom Meeting Analytics Development

fathom-local-dev-loop

jeremylongshore/claude-code-plugins-plus-skills

This setup provides a local development loop for integrating and testing Fathom API functionalities. It utilizes mock meeting and transcript data, making it ideal for building meeting analytics tools, simulating webhook handlers, or iterating on complex transcript processing pipelines without requiring live API calls. It ensures a robust environment for isolated development testing.

Flexport Webhook Event Handler

flexport-webhooks-events

jeremylongshore/claude-code-plugins-plus-skills

Implements robust webhook event handling for Flexport, enabling real-time tracking and processing of critical logistics updates. It manages shipment milestones (e.g., departed, arrived, delivered), booking confirmations, PO changes, and invoice events. Includes signature verification (HMAC-SHA256) and idempotent processing to ensure reliable supply chain data integration.

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