# sleuth

> research software for RNA sequencing

**Wikidata**: [Q122830809](https://www.wikidata.org/wiki/Q122830809)  
**Source**: https://4ort.xyz/entity/sleuth-q122830809

## Summary
Sleuth is research software designed specifically for RNA sequencing analysis. It enables researchers to perform differential analysis of RNA-seq data while incorporating quantification uncertainty for more accurate results.

## Key Facts
- Sleuth is an open-source research software for RNA sequencing analysis
- It is licensed under GNU General Public License version 3.0
- The software is developed by Pachter Lab, with its source code available on GitHub
- The current stable version is 0.30.2, released on May 28, 2025
- Sleuth was designed to perform differential analysis of RNA-seq incorporating quantification uncertainty
- The software website is https://pachterlab.github.io/sleuth/ and is primarily in English
- The software was originally described in the publication "Differential analysis of RNA-seq incorporating quantification uncertainty"
- It is copyrighted software, not in the public domain

## FAQs
### Q: What is sleuth used for?
A: Sleuth is research software specifically designed for RNA sequencing analysis. It enables researchers to perform differential analysis of RNA-seq data while incorporating quantification uncertainty for more accurate results.

### Q: Who developed sleuth?
A: Sleuth was developed by Pachter Lab, a research group likely associated with Lior Pachter who was mentioned in the original description post from 2015.

### Q: What is the license for sleuth?
A: Sleuth is licensed under GNU General Public License version 3.0, which means it is free software with certain copyleft requirements.

### Q: When was the latest version of sleuth released?
A: The current stable version of sleuth is 0.30.2, which was released on May 28, 2025.

### Q: How does sleuth differ from other RNA-seq analysis tools?
A: Sleuth specifically incorporates quantification uncertainty into its differential analysis of RNA-seq data, which distinguishes it from other tools that may not account for this statistical aspect.

## Why It Matters
Sleuth represents an important advancement in computational biology by providing a specialized tool for RNA sequencing analysis that accounts for quantification uncertainty. This statistical approach leads to more accurate and reliable results in differential gene expression analysis, which is crucial for understanding biological processes and disease mechanisms. The software has been adopted by researchers worldwide since its inception, contributing to numerous scientific discoveries in genomics and transcriptomics. Its open-source nature and regular updates ensure continued improvement and accessibility, making it a valuable resource in the bioinformatics community.

## Notable For
- Incorporating quantification uncertainty into RNA-seq differential analysis for more accurate results
- Being developed by Pachter Lab, a recognized authority in computational biology
- Having a consistent release history with stable versions dating back to 2015 and continuing through 2025
- Utilizing the GNU General Public License version 3.0, ensuring open access while maintaining software freedom
- Having comprehensive documentation and a dedicated website for user support and information

## Body
### Development and Origin
Sleuth was developed by Pachter Lab, with its first stable version (0.27.3) released on October 22, 2015. The software was originally described in the publication "Differential analysis of RNA-seq incorporating quantification uncertainty," highlighting its unique approach to statistical analysis in RNA sequencing.

### Technical Specifications
- Type: Research software for RNA sequencing
- License: GNU General Public License version 3.0
- Copyright status: Copyrighted software
- Language: Primarily English, as reflected in its website
- Source code repository: https://github.com/pachterlab/sleuth
- Official website: https://pachterlab.github.io/sleuth/

### Version History
Sleuth has undergone regular development with multiple stable releases:
- Version 0.27.3 (stable): Released October 22, 2015
- Version 0.28.0 (stable): Released October 28, 2015
- Version 0.28.1 (stable): Released June 20, 2016
- Version 0.29.0 (stable): Released May 29, 2017
- Version 0.30.0 (stable): Released June 8, 2018
- Version 0.30.1 (stable): Released November 14, 2022
- Version 0.30.2 (stable, current): Released May 28, 2025

### Functionality and Use
Sleuth is specifically designed for RNA-Seq (RNA sequencing) analysis, with a focus on differential analysis that incorporates quantification uncertainty. This statistical approach distinguishes it from other RNA-seq analysis tools and provides more accurate results when identifying differentially expressed genes or transcripts.

### Documentation and Support
The software is well-documented with an official website that provides information about its features, usage, and updates. The GitHub repository serves as the primary platform for source code access, issue reporting, and community contributions.

## References

1. [Source](https://github.com/pachterlab/sleuth/commit/419b0c05e0c7e1460b435723ad3f72172f4a5d99)
2. [Release 0.27.3. 2015](https://github.com/pachterlab/sleuth/releases/tag/v0.27.3)
3. [Release 0.28.0. 2015](https://github.com/pachterlab/sleuth/releases/tag/v0.28.0)
4. [Release 0.28.1. 2016](https://github.com/pachterlab/sleuth/releases/tag/v0.28.1)
5. [Release 0.29.0. 2017](https://github.com/pachterlab/sleuth/releases/tag/v0.29.0)
6. [Release 0.30.0. 2018](https://github.com/pachterlab/sleuth/releases/tag/v0.30.0)
7. [Release 0.30.1. 2022](https://github.com/pachterlab/sleuth/releases/tag/v0.30.1)
8. [Release 0.30.2. 2025](https://github.com/pachterlab/sleuth/releases/tag/v0.30.2)