Package: HeritSeq 1.0.1

W. Jenny Shi

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.

Authors:W. Jenny Shi [aut, cre], Pamela Russell [aut], Pratyaydipta Rudra [aut, cre], Brian Vestal [aut, cre], Katerina Kechris [aut], Laura Saba [aut]

HeritSeq_1.0.1.tar.gz
HeritSeq_1.0.1.zip(r-4.5)HeritSeq_1.0.1.zip(r-4.4)HeritSeq_1.0.1.zip(r-4.3)
HeritSeq_1.0.1.tgz(r-4.4-any)HeritSeq_1.0.1.tgz(r-4.3-any)
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HeritSeq.pdf |HeritSeq.html
HeritSeq/json (API)

# Install 'HeritSeq' in R:
install.packages('HeritSeq', repos = c('https://kechrislab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kechrislab/heritseq/issues

Datasets:
  • para_cp - Parameter matrix obtained from simData by fitting CPMM.
  • para_nb - Parameter matrix obtained from simData by fitting NBMM.
  • simData - A simulated sequencing dataset.
  • simData_voom - Voom transformed version of simData.
  • simData_vst - Variance stabilize transformed version of simData.
  • strains - List of strain names for the samples.
  • weights_voom - Weights used in the voom transformation.

On CRAN:

2.60 score 2 stars 8 scripts 164 downloads 1 mentions 8 exports 82 dependencies

Last updated 6 years agofrom:262f1e83a3. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 18 2024
R-4.5-winWARNINGOct 18 2024
R-4.5-linuxWARNINGOct 18 2024
R-4.4-winWARNINGOct 18 2024
R-4.4-macWARNINGOct 18 2024
R-4.3-winWARNINGOct 18 2024
R-4.3-macWARNINGOct 18 2024

Exports:computeVPC.CPcomputeVPC.NBfit.CPfit.NBfitComputeVPC.lmergetBootCIgetReadMatrix.CPgetReadMatrix.NB

Dependencies:abindaskpassBHbiglmBiobaseBiocGenericsBiocParallelbootclicodacodetoolscolorspacecplmcpp11crayoncurlDBIDelayedArrayDESeq2fansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4locfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeminqamunsellnlmenloptropensslpbapplypillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletweedieUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc