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consistent quantification of external RNA-seq data sets
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bulk_rnaseq/data-raw/EGEUV1 Added data sets Jun 20, 2017
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00_help_functions.R small tweak to get the colData() properly out of Charlotte's object Mar 26, 2018
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02_process_data.R add functions to compile TCC into SummarizedExperiment object Mar 26, 2018
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04_run_data_processing_bulk.R Updated README, added possibility to save to specified location. May 31, 2017
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directory_setup create -k 15 kallisto index for mouse, setup GSE52529-GPL16791, GSE60… Mar 13, 2018
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README.md

conquer

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

Adapters

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).

Contact

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

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