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https://github.com/markrobinsonuzh/conquer
consistent quantification of external RNA-seq data sets
https://github.com/markrobinsonuzh/conquer
Last synced: 3 days ago
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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 (about 1 year ago)
- Last Synced: 2024-03-15T19:10:12.873Z (10 months ago)
- Language: HTML
- Size: 2.44 MB
- Stars: 54
- Watchers: 6
- Forks: 14
- Open Issues: 0
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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]).