Title: Splicing Efficiency Analysis and Annotation
Description: The aim of 'SEAA' is to provide convenient and rapid splicing
efficiency calculation and splicing sites annotation function using next
generation sequencing data. Aligned files and a processed splicing sites
annotation file are needed. The task can be finished in several minutes
using multi-core computing with the assistance of 'Rsubread'. Plots of
splicing status type and Cumulative Distribution Function (CDF) and
annotated valid splicing efficiency can be exported.
Imports: clusterProfiler, ggforce, ggplot2, ggpubr, ggrepel, grDevices,
gridExtra, org.Hs.eg.db, org.Mm.eg.db, reshape2, Rsubread,
Author: Zixiang Wang [aut, cre] (<https://orcid.org/0000-0001-5252-9764>),

Title: Scalable Exact Algorithm for Large-Scale Set-Based GxE Tests
Authors@R: c(person("Jocelyn", "Chi", email = "jocetchi@gmail.com",
person("Ilse", "Ipsen", email = "ipsen@ncsu.edu",
person("Jung-Ying", "Tzeng", email = "jytzeng@ncsu.edu",
The explosion of biobank data offers immediate opportunities for
gene-environment (GxE) interaction studies of complex diseases because of the
large sample sizes and rich collection in genetic and non-genetic information.
However, the extremely large sample size also introduces new computational
challenges in GxE assessment, especially for set-based GxE variance component (VC)
tests, a widely used strategy to boost overall GxE signals and to evaluate the
joint GxE effect of multiple variants from a biologically meaningful unit
We present 'SEAGLE', a Scalable Exact AlGorithm for Large-scale Set-based
GxE tests, to permit GxE VC test scalable to biobank data. 'SEAGLE' employs modern
matrix computations to achieve the same “exact” results as the original GxE VC
tests, and does not impose additional assumptions nor relies on approximations.
'SEAGLE' can easily accommodate sample sizes in the order of 10^5, is implementable
on standard laptops, and does not require specialized equipment.
The accompanying manuscript for this package can be found at Chi, Ipsen, Hsiao,
Depends: R (>= 3.5.0), Matrix, CompQuadForm