Package: PQLseq 1.2.1
Jiaqiang Zhu
PQLseq: Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies
An efficient tool designed for differential analysis of large-scale RNA sequencing (RNAseq) data and Bisulfite sequencing (BSseq) data in the presence of individual relatedness and population structure. 'PQLseq' first fits a Generalized Linear Mixed Model (GLMM) with adjusted covariates, predictor of interest and random effects to account for population structure and individual relatedness, and then performs Wald tests for each gene in RNAseq or site in BSseq.
Authors:
PQLseq_1.2.1.tar.gz
PQLseq_1.2.1.tar.gz(r-4.5-noble)PQLseq_1.2.1.tar.gz(r-4.4-noble)
PQLseq_1.2.1.tgz(r-4.4-emscripten)PQLseq_1.2.1.tgz(r-4.3-emscripten)
PQLseq.pdf |PQLseq.html✨
PQLseq/json (API)
| # Install 'PQLseq' in R: |
| install.packages('PQLseq', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- ExampleBSseq - BSseq example dataset
- ExampleRNAseq - RNAseq example dataset
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:0463c810bc. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 15 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 15 2024 |
Exports:pqlseq
Dependencies:codetoolsdoParallelforeachiteratorslatticeMatrixRcppRcppArmadillo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies | PQLseq-package PQLseq |
| BSseq example dataset | ExampleBSseq |
| RNAseq example dataset | ExampleRNAseq |
| Fit Generalized Linear Mixed Model with Known Kinship Matrices Through Penalized-quasi Likelihood | pqlseq |