Published November 29, 2022
| Version 1
Software
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Software for the manuscript "Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases"
Authors/Creators
- de Klein, Niek1
- Tsai, Ellen A.2
- Vochteloo, Martijn1
- Baird, Denis2
- Huang, Yunfeng2
- Chen, Chia-Yen2
- van Dam , Sipko1
- Oelen, Roy1
- Deelen, Patrick1
- Bakker, Olivier B.1
- El Garwany, Omar1
- Ouyang, Zhengyu2
- Marshall, Eric E.2
- Zavodszky, Maria I.2
- van Rheenen , Wouter3
- Bakker, Mark K.3
- Veldink, Jan3
- Gaunt, Tom R.4
- Runz, Heiko2
- Franke, Lude1
- Westra, Harm-Jan1
- 1. Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, The Netherlands
- 2. Translational Biology, Research & Development, Biogen Inc., 225 Broadway, Cambridge, MA, USA
- 3. Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- 4. MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
Description
Jar executables and scripts to process data, call cis- and trans-eQTLs and make figures for our manuscript "Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases".
- eqtl-mapping-pipeline.jar: eQTL mapping software to run eQTL mapping as was done in eQTLgen1 and in our MetaBrain preprint2. Source code is located at: https://github.com/molgenis/systemsgenetics/tree/master/eqtl-mapping-pipeline/
- MbQTL-1.1-SNAPSHOT-jar-with-dependencies.jar: eQTL mapping software to run eQTL mapping with FDR estimiation similar to FastQTL3. Source code is located at: https://github.com/molgenis/systemsgenetics/tree/master/mbQTL
See our manuscript for a detailed description of the difference in methods.
- metabrain-master.zip: Scripts used for downloading and processing RNA-seq and genotype data, predicting cell propotions, interaction eQTL, other analysis and for generating figures. This zip is a copy of https://github.com/molgenis/metabrain/ made on 26/11/2022