RNAlysis 3.11.0 documentation

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

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About RNAlysis:

• What is RNAlysis?
• What can I do with RNAlysis?
• 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
  • Open the program
  • Load a table
  • Examine your table
  • Filter your table
  • Undo the operations you applied to your table
  • Apply your operations ‘in-place’ or apply on a new table
  • Save the changes you made to your table
  • Work on multiple tables at the same time
  • Different types of tables offer different ways to filter and analyze your data
  • Create and save graphs
  • Quickly look-up genes in your database of choice
  • Sort your tabs and change their icons
  • Restore tabs you closed
  • Import lists of genes as Gene Sets
  • Visualize the intersections between your tables and gene sets
  • Apply set operations to your tables and gene sets
  • Perform enrichment analysis on your tables and gene sets
  • Create Pipelines to streamline your data analysis
  • Apply Pipelines to one or more of your tables
  • Export and share Pipelines to make your analysis more reproducible
  • Interface with other bioinformatic tools
  • Create an interactive analysis report
• A-to-Z tutorial - example analysis
  • Intro and recommendations
  • Analysis #1 - time series RNA sequencing
  • Analysis #2 - differential expression data
  • Final words
• 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
  • 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