Published February 23, 2024
| Version v1
Software
Open
scAlleleExpression: R package for downstream analysis of allele specific expression single cell data
Contributors
Researchers:
- Simmons, Sean
- Adiconis, Xian
- Haywood, Nathan
- Parker, Jacob
- Liao, Zhixiang
- Tuncali, Idil
- Al'Khafaji, Aziz
- Shin, Asa
- Jagadeesh, Karthik
- Gosik, Kirk
- Gatzen, Michael
- Smith, Jonn
- El Kodsi, Daniel
- Kuras, Yuliya
- Baecher-Allan, Clare
- Serrano, Geidy
- Beach, Thomas
- Garimella, Kiran
- Rozenblatt-Rosen, Orit
- Regev, Aviv
- Dong, Xianjun
- Scherzer, Clemens
- Levin, Joshua
Description
This R package is build to use single cell or nuclei allele specific expression (ASE) data to investigate Cell Type specific regulatory genetics (eQTLs, etc). It is build to work with the output of our ASE pipeline (https://github.com/seanken/ASE_pipeline), but ourdownstream analysis tools should work with most allele specific expression pipelines.
The package is built to:
- Load the output of our ASE pipeline into a matrix or a Seurat object.
- Load snps or gene level allele specific expression information in either a pseudobulk or cell specific count matrix.
- Perform varying types of allele specific expression analysis.
Tasks 1 and 2 are pipeline specific, but taks 3 is more general.
Files
scAlleleExpression-main.zip
Files
(31.2 kB)
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Additional details
Funding
- Aligning Science Across Parkinson's
- Parkinson5D: deconstructing proximal disease mechanisms across cells, space, and progression ASAP-000301
Software
- Repository URL
- https://github.com/seanken/scAlleleExpression
- Programming language
- R
- Development Status
- Wip