RNAlysis 4.1.0 documentation

Useful links: Documentation | Source code | Bug reports | | | | |

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About RNAlysis:

• 🧬 What is RNAlysis?
• 🎥 See RNAlysis in Action
• 🚀 Key Features
• 🛠️ How do I install it?
• 📊 How do I use it?
• Dependencies
• Credits
  • How do I cite RNAlysis?
  • Development Lead
  • Contributors
• GitHub page
• How can I contribute to RNAlysis?
  • Types of Contributions
  • Get Started!
  • Pull Request Guidelines
  • Tips
  • Deploying

Starting with RNAlysis:

• Installation
  • RNAlysis stand-alone app (most beginner-friendly)
  • Install as a Python package with pip (best performance)
  • From sources
• RNAlysis quick-start video guide
  • Launching RNAlysis
  • Importing Data
  • Exploring Your Dataset
  • Applying Filters
  • Undo the operations you applied to your data
  • Apply your operations ‘in-place’ or make a copy
  • Generating and Saving Visualizations
  • Analyze Multiple Tables at the Same Time
  • Organizing Your Workspace
  • Saving Modified Tables
  • Creating Gene Sets
  • Visualizing Gene Set Intersections
  • Performing Set Operations
  • Conducting Enrichment Analysis
  • Rapid Gene Information Lookup
  • Building Analysis Pipelines
  • Executing Pipelines
  • Sharing and Reproducing Analyses
  • Integrating External Bioinformatic Tools
  • Leveraging Table-Specific Functions
  • Recovering Closed Tabs
  • Generating Interactive Analysis Reports
• A-to-Z tutorial - example analysis
  • Intro and recommendations
  • Analysis #1 - time series RNA sequencing
  • Analysis #2 - differential expression data
  • Final words
• How to use the RNAlysis analysis reports
  • Understanding the Graph
  • Node Details at a Glance
  • Accessing Associated Files
  • Navigating the Graph: Panning
  • Navigating the Graph: Zooming
  • Fitting the Graph to View
  • Tracing Analysis Paths
  • Filtering by Node Type
• Frequently asked questions
  • Installation
  • Usage
  • Automatic analysis reports
• User guide - graphical interface
  • Analyzing data tables with RNAlysis
  • RNAlysis Gene Sets module
  • RNAlysis interactive analysis reports
  • RNAlysis settings
• User guide - programmatic interface
  • RNAlysis fastq module
  • RNAlysis filtering module
  • RNAlysis enrichment module
  • RNAlysis general module
• Glossary - programmatic interface

Change history:

• History
  • 4.1.0 (2024-09-16)
  • 4.0.0 (2024-06-29)
  • 3.12.0 (2024-05-14)
  • 3.11.0 (2024-01-05)
  • 3.10.1 (2023-11-22)
  • 3.10.0 (2023-10-31)
  • 3.9.2 (2023-06-23)
  • 3.9.1 (2023-06-19)
  • 3.9.0 (2023-06-09)
  • 3.8.0 (2023-05-07)
  • 3.7.0 (2023-04-07)
  • 3.6.2 (2023-03-25)
  • 3.6.1 (2023-03-22)
  • 3.6.0 (2023-03-07)
  • 3.5.2 (2023-02-23)
  • 3.5.1 (2023-02-22)
  • 3.5.0 (2023-02-08)
  • 3.4.2 (2023-02-01)
  • 3.4.0 (2023-02-01)
  • 3.3.0 (2022-12-02)
  • 3.2.2 (2022-11-25)
  • 3.2.1 (2022-11-25)
  • 3.2.0 (2022-11-23)
  • 3.1.0 (2022-10-16)
  • 3.0.1 (2022-10-12)
  • 3.0.0 (2022-10-10)
  • 2.1.1 (2022-07-05)
  • 2.1.0 (2022-04-16)
  • 2.0.1 (2022-04-02)
  • 2.0.0 (2021-12-05)
  • 1.3.5 (2020-05-27)
  • 1.3.4 (2020-04-07)
  • 1.3.3 (2020-03-28)
  • 1.3.2 (2019-12-11)

Modules:

rnalysis.fastq	The fastq module provides a unified programmatic interface to external tools that process FASTQ files.
rnalysis.filtering	This module can filter, normalize, intersect and visualize tabular data such as read counts and differential expression data.
rnalysis.enrichment	This module can perform enrichment analyses on a given set of genomic features and visualize their intersections.
rnalysis.general	This module contains general-purpose functions.

Indices and tables:

• Index
• API Reference