https://github.com/markrobinsonuzh/conquer

consistent quantification of external RNA-seq data sets
https://github.com/markrobinsonuzh/conquer

Last synced: about 1 month ago
JSON representation

consistent quantification of external RNA-seq data sets

• Host: GitHub
• URL: https://github.com/markrobinsonuzh/conquer
• Owner: markrobinsonuzh
• License: mit
• Created: 2016-07-22T11:47:31.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2023-12-21T06:04:59.000Z (12 months ago)
• Last Synced: 2024-03-15T19:10:12.873Z (9 months ago)
• Language: HTML
• Size: 2.44 MB
• Stars: 54
• Watchers: 6
• Forks: 14
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: License.md

Awesome Lists containing this project

• Awesome-Bioinformatics-Benchmarks - conquer

README

        
# conquer

This repository contains the code used to prepare the *conquer* (**con**sistent **qu**antification of **e**xternal **R**NA-seq data sets) repository, which provides access to consistently processed, analysis-ready single-cell RNA-seq data sets, together with quality control and exploratory analysis reports to help the user determine whether a particular data set fits their purposes. 

The repository is available at [http://imlspenticton.uzh.ch:3838/conquer/](http://imlspenticton.uzh.ch:3838/conquer/). A more detailed description of the workflow that was used to process the data is available in the publication listed below, within the application (see the "About" tab), and [here](shiny-download/about_conquer.md).

If you use *conquer*, please cite

* C Soneson & MD Robinson: [Bias, robustness and scalability in single-cell differential expression analysis](https://www.nature.com/articles/nmeth.4612). Nature Methods (2018).

## Adapters

In cases where adapter trimming was necessary, we used a fasta file with adapters obtained from [https://github.com/csf-ngs/fastqc/blob/master/Contaminants/contaminant_list.txt](https://github.com/csf-ngs/fastqc/blob/master/Contaminants/contaminant_list.txt) (downloaded on July 25, 2016).

## Contact

If you have questions or comments about *conquer*, please contact [Charlotte Soneson](mailto:[email protected]) or [Mark D Robinson](mailto:[email protected]).