HeritSeq

Heritability of Gene Expression for Next-Generation Sequencing

Statistical framework to analyze heritability of gene expression based on next-generation sequencing data and simulating sequencing reads. Variance partition coefficients (VPC) are computed using linear mixed effects and generalized linear mixed effects models. Compound Poisson and negative binomial models are included. Reference: Rudra, Pratyaydipta, et al. "Model based heritability scores for high-throughput sequencing data." BMC bioinformatics 18.1 (2017): 143.

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Description file content

Package
HeritSeq
Title
Heritability of Gene Expression for Next-Generation Sequencing
Version
1.0.1
Date
2019-02-11
Author
W. Jenny Shi [aut, cre], Pamela Russell [aut], Pratyaydipta Rudra [aut, cre], Brian Vestal [aut, cre], Katerina Kechris [aut], Laura Saba [aut]
Maintainer
W. Jenny Shi
Description
Statistical framework to analyze heritability of gene expression based on next-generation sequencing data and simulating sequencing reads. Variance partition coefficients (VPC) are computed using linear mixed effects and generalized linear mixed effects models. Compound Poisson and negative binomial models are included. Reference: Rudra, Pratyaydipta, et al. "Model based heritability scores for high-throughput sequencing data." BMC bioinformatics 18.1 (2017): 143.
BugReports
https://github.com/KechrisLab/HeritSeq/issues
Depends
R (>= 3.2.3)
License
GPL-2
Encoding
UTF-8
LazyData
true
Imports
cplm, DESeq2, lme4, pbapply, tweedie, MASS, SummarizedExperiment
Suggests
glmmADMB
Additional_repositories
http://glmmadmb.r-forge.r-project.org/repos
RoxygenNote
5.0.1
NeedsCompilation
no
Packaged
2019-02-11 16:59:28 UTC; wenjennyshi
Repository
CRAN
Date/Publication
2019-02-11 21:13:29 UTC

install.packages('HeritSeq')

1.0.1

2 months ago

W. Jenny Shi

GPL-2

Depends on

R (>= 3.2.3)

Imports

cplm, DESeq2, lme4, pbapply, tweedie, MASS, SummarizedExperiment

Suggests

glmmADMB

Discussions