Cis-GS Documentation

Cis-regulatory Element Genome Scanner — a whole-genome pipeline for discovering cis-regulatory elements, coupling them to expression, and finishing with KEGG enrichment, in one PyQt5 desktop app and one interactive CLI.

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Quick links

• Installation — pip, standalone .exe, from source

• Quick Start — one-minute GUI + CLI walkthrough

• The 7-Step Workflow — the 7-step scientific pipeline

• GUI Overview — every tab of the PyQt5 desktop app explained

• CLI Overview — cis-gs command reference

• Programmatic API — programmatic Python API

Getting Started

• Installation
  • From PyPI (recommended)
  • Standalone Windows executable
  • From source (for development)
  • First-run setup
• Quick Start
  • GUI in 5 clicks
  • CLI wizard
  • One-liner CLI examples

Scientific Workflow

• The 7-Step Workflow
• Step 1 — Promoter Extraction
  • Inputs
  • What it does
  • Output
  • CLI equivalent
• Step 2 — Motif Search
  • Inputs
  • Statistics
  • Outputs
  • Gene-ID Resolution
• Step 3 — Motif Logos
  • Inputs
  • Settings
  • Outputs
• Step 4 — Expression Feeding
  • Inputs
  • Gene-ID Mapping Methods
  • Outputs
• Step 5 — Co-expression Network
  • Inputs
  • Pipeline
  • Outputs
• Step 6 — K-means Clustering
  • Inputs
  • Settings
  • Diagnostics
  • Outputs
• Step 7 — KEGG Enrichment
  • Inputs
  • Statistics
  • REST endpoints used
  • Output
  • CLI equivalent

GUI

• GUI Overview
  • Theme & shortcuts
• NCBI Fetch Tab
  • Search strategies
  • Outputs
• Contact Tab
  • Theming

CLI

• CLI Overview
  • Conveniences
• The Wizard
  • Sample session
• Command Reference
  • cis-gs fetch
  • cis-gs extract
  • cis-gs search
  • cis-gs feed
  • cis-gs coexpr
  • cis-gs kmeans
  • cis-gs enrich-kegg
  • cis-gs id-convert

API Reference

• Programmatic API
  • cis_gs.enrichment
  • cis_gs.enrichment.idmap
  • Top-level package
• cis_gs.enrichment
  • cis_gs.enrichment.core
  • cis_gs.enrichment.kegg
  • cis_gs.enrichment.plots
• cis_gs.enrichment.idmap
  • detect_id_type()
  • consensus_id_type()
  • IDMapping
  • IDConverter
  • search_ncbi_taxonomy()

Project

• Changelog
• Contributing
• Citation

Indices

• Index

• Module Index

• Search Page