sQTLseekeR2-package: sQTLseekeR2: R package for splicing QTL mapping

In guigolab/sQTLseekeR2: R package for splicing QTL mapping

Description

sQTLseekeR2 tests for association between genetic variants and alternative splicing (relative transcript abundances of a gene measured from RNA-seq), using a multivariate non-parametric approach. It is an enhanced version of sQTLseekeR (see Details).

Details

Main enhancements in sQTLseekeR2:

• Covariate correction

• Faster pre-processing of transcript expression

• Improved P-value calculation with higher precision

• Permutation-based schema for multiple testing correction

• LD-based variant clustering

Author(s)

Diego Garrido-Martín, Jean Monlong, Miquel Calvo, Ferran Reverter, Roderic Guigó

References

Garrido-Martín, D. et al. Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. Nat Commun 12, 727 (2021). https://doi.org/10.1038/s41467-020-20578-2

See Also

Useful links:

• https://github.com/guigolab/sQTLseekeR2

• https://github.com/guigolab/sqtlseeker2-nf

guigolab/sQTLseekeR2 documentation built on Nov. 20, 2021, 3:21 a.m.