Package: HeritSeq 1.0.1
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:
HeritSeq_1.0.1.tar.gz
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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')) |
Bug tracker:https://github.com/kechrislab/heritseq/issues
- 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.
Last updated 6 years agofrom:262f1e83a3. Checks:OK: 1 WARNING: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 18 2024 |
R-4.5-win | WARNING | Oct 18 2024 |
R-4.5-linux | WARNING | Oct 18 2024 |
R-4.4-win | WARNING | Oct 18 2024 |
R-4.4-mac | WARNING | Oct 18 2024 |
R-4.3-win | WARNING | Oct 18 2024 |
R-4.3-mac | WARNING | Oct 18 2024 |
Exports:computeVPC.CPcomputeVPC.NBfit.CPfit.NBfitComputeVPC.lmergetBootCIgetReadMatrix.CPgetReadMatrix.NB
Dependencies:abindaskpassBHbiglmBiobaseBiocGenericsBiocParallelbootclicodacodetoolscolorspacecplmcpp11crayoncurlDBIDelayedArrayDESeq2fansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4locfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeminqamunsellnlmenloptropensslpbapplypillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletweedieUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc