Results for “cli”

Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

The English summary is being prepared. Showing the original description.

Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

The English summary is being prepared. Showing the original description.

Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

The English summary is being prepared. Showing the original description.

Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

The English summary is being prepared. Showing the original description.

Track pull requests opened by a Paperclip instance, explain their purpose, and assess whether their latest changes are ready to merge. Dispatch preparation work for unresolved problems and publish an evidence-based report without merging anything.

• Reviewing readiness across an instance's open pull requests
• Dispatching preparation work for failing checks or conflicts
• Checking readiness again after fixes

Guide development of new interaction cards in Paperclip issue threads, such as approvals or structured questions. Covers shared data definitions, server behavior, interface states, CLI and MCP support, plugin helpers, documentation, and tests.

• Adding an approval card to an issue thread
• Creating an interaction with a new response format
• Checking implementation coverage across layers

Automate Clickmeeting operations through Rube MCP, a connection for agent tools. The skill discovers available actions, checks the account connection, and uses current input requirements to carry out the requested workflow.

• Finding available Clickmeeting actions
• Automating routine Clickmeeting operations
• Running multiple operations in one workflow

Learn GitHub Copilot CLI through interactive lessons for developers and non-developers. Practice prompts, permissions, file references, and task planning, with progress tracking and answers to specific questions as you work through the material.

• Learning Copilot CLI basics step by step
• Practicing writing and summaries without coding
• Learning file references and planning commands

Find and call Feishu or Lark APIs when existing skills and CLI commands do not cover a task. Follow official documentation to identify the endpoint, required inputs, permissions, and a complete lark-cli command example.

• Find APIs missing from existing CLI commands
• Check API parameters and required permissions
• Add chat members through a documented API

Automate Clickmeeting operations through Rube MCP, a connection for agent tools. The skill discovers available actions, checks the account connection, and uses current input requirements to carry out the requested workflow.

• Finding available Clickmeeting actions
• Automating routine Clickmeeting operations
• Running multiple operations in one workflow

Search ClinVar and NCBI Variation for genetic variants, or look up records using VCV, RCV, SCV, and RefSNP identifiers. Get concise summaries, check identifier mappings, and save full JSON responses when needed.

• Searching ClinVar for a genetic variant
• Looking up VCV, RCV, SCV, or RefSNP records
• Checking mappings between variant identifiers

Search ClinicalTrials.gov studies by condition and recruitment status, then receive concise summaries. Use the same client to inspect API field definitions, allowed values, search areas, and field statistics, with an option to save raw responses.

• Finding recruiting studies for a specific condition
• Getting concise summaries of clinical trial search results
• Checking API field definitions and allowed values

Prepare Paperclip changes for a pull request by organizing commits, updating the branch, writing the description, addressing automated review feedback, and checking tests and CI before reporting the result for handoff.

• Preparing completed Paperclip changes for review
• Resolving Greptile feedback and failed checks
• Splitting large changes into separate pull requests

Use an assigned Slack bot to read shared conversations, search accessible discussions, summarize with source links, and send messages or files. It connects Slack collaboration with Paperclip tasks and routines while respecting channel access and delivery status.

• Summarize channel discussions with source links
• Search accessible messages and read thread replies
• Send results or files through the assigned bot

Manage an AI-agent company in Paperclip through conversation. Set up the company, hire and configure agents, handle approvals, track tasks and spending, and review work products, with summaries and links to the relevant web pages.

• Setting up a company and its CEO agent
• Planning agent hires and reporting relationships
• Reviewing pending approvals and stalled tasks

Manage work on a SeaClip-Lite project board through commands that create and update issues, control pipelines, configure schedules, and inspect recent activity, with JSON output for AI agents.

• Find issues by status or priority
• Create issues and move them between board columns
• Start, resume, or stop work pipelines

Use Reasonix to build or improve a Python command-line interface for existing software. The workflow covers source analysis, interactive commands, JSON output, tests, documentation, and installation checks using the software’s own backend where possible.

• Build command-line access to a GUI application
• Add missing features to an existing command-line interface
• Test commands against the actual software backend

Delegate repository analysis and coding tasks to Gemini CLI without an interactive session. The skill reads its structured results, summarizes responses and errors, and supports comparing Gemini’s work with another coding agent.

• Reviewing a module without editing files
• Delegating coding tasks to Gemini CLI
• Comparing results from different coding agents

Helps build or improve reusable OpenCLI website commands in JavaScript. It uses observed page behavior, captured requests, and existing adapters to guide implementation, then checks definitions and tests real command behavior and failure handling.

• Turning repeated website tasks into OpenCLI commands
• Improving an existing website adapter
• Investigating API requests before implementation

Helps agents find and use OpenCLI commands for websites and Chrome. It guides command discovery, input checks, result interpretation, and error recovery so agents can select suitable browser tools or reusable website commands.

• Finding OpenCLI commands for a specific website
• Checking command inputs and output formats
• Diagnosing Chrome connection problems

Inspect and manage Tencent Cloud resources with tccli, its command line tool. Covers servers, networking, DNS, certificates, permissions, monitoring, and application deployment, with supporting scripts for login and identifying the current cloud instance.

• Checking Lighthouse and CVM server status
• Reviewing domain expiry dates and SSL certificates
• Inspecting security groups and access permissions

Design or change REA investigation tools by defining responsibilities, inputs, results, and CLI or MCP interfaces. Produce a proposal that explains how Evidence records should be interpreted, compares the nearest existing alternative, and outlines verification.

• Designing a new REA investigation tool
• Reviewing CLI or MCP inputs and results
• Defining provider responsibilities and Evidence meaning

Helps design ClickHouse tables, write analytical queries, and improve slow queries. Covers loading data in batches, preparing reusable summaries, and monitoring performance for large datasets, real-time dashboards, and time-series analysis.

• Designing tables for large-scale analytics
• Improving slow aggregation queries
• Loading large datasets in batches

Verify Paperclip through real browser or command-line journeys across source checkouts, published npm installations, or existing hosted environments. Record the exact version, platform, starting data, observed behavior, and supporting evidence for each tested journey.

• Checking first-time installation and onboarding
• Verifying features with fresh or existing data
• Testing a specific published npm version