This repository contains the code used to prepare the conquer (consistent quantification of external RNA-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/. 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.
If you use conquer, please cite
- C Soneson & MD Robinson: Bias, robustness and scalability in single-cell differential expression analysis. Nature Methods (2018).
In cases where adapter trimming was necessary, we used a fasta filew ith adapters obtained from https://github.com/csf-ngs/fastqc/blob/master/Contaminants/contaminant_list.txt (downloaded on July 25, 2016).