Published August 16, 2024
| Version 1.0
Software
Open
Mapping single cell eQTLs by using MatrixEQTL with pseudo-bulk cell type
Authors/Creators
-
1.
Yale University
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2.
Yale School of Medicine
Description
These scripts are implementing a two-step approach for detecting eQTL and conditional eQTL analysis for cell type gene expression in single cell RNA seq study.
Relevant R packages: SVA (version 3.52.0, DOI: 10.18129/B9.bioc.sva), MatrixEQTL (version 2.1.0, link: https://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/runit.html)
optparse (version 1.7.5, for passing parameters from command line, link: https://cran.r-project.org/web/packages/optparse/index.html)
Additional information, pls see the README file.
Files
covariants_100_samples_with_first_three_sva_factors.txt
Files
(53.2 kB)
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Additional details
Identifiers
Related works
- Is derived from
- Journal: 10.1093/bioinformatics/bts163 (DOI)
- Journal: 10.1093/bioinformatics/bts034 (DOI)
Funding
- Aligning Science Across Parkinson's
- PD5D decoding Parkinson's in five dimensions: single cell eQTL study ASAP-000301
Dates
- Available
-
2024-08-12
Software
- Programming language
- R