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consistent quantification of external RNA-seq data sets
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Latest commit 6708722 May 26, 2018
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bulk_rnaseq/data-raw/EGEUV1 Added data sets Jun 20, 2017
data-raw Exclude a few unavailable samples Jan 23, 2018
00_help_functions.R small tweak to get the colData() properly out of Charlotte's object Mar 26, 2018
02_process_data.R add functions to compile TCC into SummarizedExperiment object Mar 26, 2018
03_run_data_processing.R Merge May 26, 2018
04_run_data_processing_bulk.R Updated README, added possibility to save to specified location. May 31, 2017
05_umi_functions.R Added data sets. Updated documentation. Allow scrolling horizontally … Sep 28, 2017 Create May 31, 2017 Update Mar 19, 2018
directory_setup create -k 15 kallisto index for mouse, setup GSE52529-GPL16791, GSE60… Mar 13, 2018
scater_template.Rmd Fixed scater template for ERCC plots Jan 24, 2018
stream_ena Added link to code in app. Added GSE41265 Sep 8, 2016


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 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


In cases where adapter trimming was necessary, we used a fasta filew ith adapters obtained from (downloaded on July 25, 2016).


If you have questions or comments about conquer, please contact Charlotte Soneson or Mark D Robinson.

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