Update SLURM documentation and related setup

Author: Linfeng Hu

DESCRIPTION

@@ -1,24 +1,55 @@
 Package: SAIGEQTL
 Type: Package
-Title: scalable and accurate expression quantitative trait locus mapping for single-cell studies
+Title: Scalable and Accurate Expression Quantitative Trait Locus Mapping
+    for Single-Cell Studies
 Version: 0.3.5
 Date: 2025-12-08
 Authors@R: c(
     person("Wei", "Zhou", email = "[email protected]", role = c("cre", "aut")),
     person("Anna", "Cuomo", email = "[email protected]", role = c("aut", "ctb")),
     person("Linfeng", "Hu", email = "[email protected]", role = c("aut", "ctb"))
 )
-Maintainer: Wei Zhou <[email protected]> 
-Description:an R package that implements the Scalable and Accurate Implementation of Generalized Poisson mixed model for eQTL mapping at the single-cell level.  
+Description: Implements the Scalable and Accurate Implementation of
+    Generalized Poisson mixed model for expression quantitative trait locus
+    (eQTL) mapping at the single-cell level. Provides functions for fitting
+    null models, performing association tests, and handling large-scale
+    single-cell genomics data efficiently.
 License: GPL (>= 2)
-Imports: Rcpp (>= 1.0.7), RcppParallel, Matrix, data.table, RcppArmadillo (>= 0.10.7.5), RcppNumerical, dbplyr, methods, optparse, RSQLite, dplyr, nlme, MASS, RhpcBLASctl
-Suggests: R.utils, furrr
-LinkingTo: Rcpp, RcppArmadillo (>= 0.10.7.5), RcppParallel, RcppEigen, BH
-Remotes: cysouw/qlcMatrix, leeshawn/MetaSKAT, barkasn/fastSave, leeshawn/SPAtest
+URL: https://github.com/weizhou0/SAIGEQTL
+BugReports: https://github.com/weizhou0/SAIGEQTL/issues
 Depends: R (>= 3.5.0)
+Imports:
+    data.table,
+    dbplyr,
+    dplyr,
+    MASS,
+    Matrix,
+    methods,
+    nlme,
+    optparse,
+    Rcpp (>= 1.0.7),
+    RcppArmadillo (>= 0.10.7.5),
+    RcppNumerical,
+    RcppParallel,
+    RhpcBLASctl,
+    RSQLite
+Suggests:
+    BiocStyle,
+    furrr,
+    knitr,
+    rmarkdown,
+    R.utils,
+    testthat (>= 3.0.0)
+LinkingTo:
+    BH,
+    Rcpp,
+    RcppArmadillo (>= 0.10.7.5),
+    RcppEigen,
+    RcppParallel
+VignetteBuilder: knitr
 SystemRequirements: GNU make
-RoxygenNote: 7.1.2
-NeedsCompilation: yes
-biocViews: Expression, GeneticVariability, Genetics, Transcriptomics, SingleCell, Regression
+biocViews: GeneExpression, GeneticVariability, Genetics, Transcriptomics,
+    SingleCell, Regression
 Encoding: UTF-8
-Packaged: 2025-12-08 EST
+NeedsCompilation: yes
+RoxygenNote: 7.1.2

NEWS.md

@@ -0,0 +1,22 @@
+# SAIGEQTL News
+
+## Version 0.3.5 (2025-12-08)
+
+### Changes
+- Updated package structure to follow Bioconductor guidelines
+- Updated DESCRIPTION file with proper formatting and metadata
+- Improved documentation
+
+## Version 0.3.4
+
+### Changes
+- Bug fixes and performance improvements
+
+## Version 0.3.0
+
+### New Features
+- Initial public release of SAIGEQTL
+- Implements Generalized Poisson mixed model for eQTL mapping
+- Support for single-cell expression data
+- Efficient handling of large-scale genomics data
+- Integration with BGEN and other genotype file formats

inst/CITATION

@@ -0,0 +1,18 @@
+citHeader("To cite SAIGEQTL in publications use:")
+
+bibentry(
+  bibtype  = "Manual",
+  title    = "SAIGEQTL: Scalable and Accurate Expression Quantitative Trait Locus Mapping for Single-Cell Studies",
+  author   = c(
+    person("Wei", "Zhou"),
+    person("Anna", "Cuomo"),
+    person("Linfeng", "Hu")
+  ),
+  year     = "2025",
+  url      = "https://github.com/weizhou0/SAIGEQTL",
+  textVersion = paste(
+    "Zhou W, Cuomo A, Hu L (2025).",
+    "SAIGEQTL: Scalable and Accurate Expression Quantitative Trait Locus Mapping for Single-Cell Studies.",
+    "R package. https://github.com/weizhou0/SAIGEQTL"
+  )
+)

tests/testthat.R

@@ -0,0 +1,5 @@
+# This file is part of the standard testthat setup
+library(testthat)
+library(SAIGEQTL)
+
+test_check("SAIGEQTL")

tests/testthat/test-placeholder.R

@@ -0,0 +1,7 @@
+# Placeholder test file
+# Add your unit tests here
+
+test_that("package loads correctly", {
+
+expect_true(requireNamespace("SAIGEQTL", quietly = TRUE))
+})

vignettes/SAIGEQTL-quickstart.Rmd

@@ -0,0 +1,101 @@
+---
+title: "SAIGEQTL: Quick Start Guide"
+author:
+- name: Wei Zhou
+- name: Anna Cuomo
+- name: Linfeng Hu
+date: "`r Sys.Date()`"
+output:
+  BiocStyle::html_document:
+    toc: true
+    toc_depth: 2
+vignette: >
+  %\VignetteIndexEntry{SAIGEQTL: Quick Start Guide}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(
+    echo = TRUE,
+    eval = FALSE,
+    message = FALSE,
+    warning = FALSE
+)
+```
+
+# Introduction
+
+SAIGEQTL implements the Scalable and Accurate Implementation of Generalized
+Poisson mixed model for expression quantitative trait locus (eQTL) mapping
+at the single-cell level.
+
+This vignette provides a quick start guide to using SAIGEQTL for eQTL
+analysis.
+
+## Installation
+
+```{r install, eval=FALSE}
+# From Bioconductor (when available)
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("SAIGEQTL")
+```
+
+## Loading the Package
+
+```{r load}
+library(SAIGEQTL)
+```
+
+# Workflow Overview
+
+A typical SAIGEQTL analysis consists of two main steps:
+
+1. **Fit the null model** using `fitNULLGLMM_multiV()`
+2. **Perform association testing** using `SPAGMMATtest()`
+
+## Step 1: Fit the Null Model
+
+The null model accounts for population structure and relatedness using a
+genetic relationship matrix (GRM).
+
+```{r fit-null, eval=FALSE}
+# Example: Fit null model
+# fitNULLGLMM_multiV(
+#     phenoFile = "phenotype.txt",
+#     phenoCol = "expression",
+#     covarColList = c("age", "sex", "PC1", "PC2"),
+#     sampleIDColinphenoFile = "sample_id",
+#     ...
+# )
+```
+
+## Step 2: Perform Association Testing
+
+After fitting the null model, perform variant-level or region-based
+association testing.
+
+```{r test, eval=FALSE}
+# Example: Run association test
+# SPAGMMATtest(
+#     modelFile = "null_model.rda",
+#     genoFile = "genotypes.bgen",
+#     outputFile = "results.txt",
+#     ...
+# )
+```
+
+# Additional Resources
+
+For detailed documentation and examples, please see:
+
+- Package documentation: `?fitNULLGLMM_multiV`, `?SPAGMMATtest`
+- GitHub repository: <https://github.com/weizhou0/SAIGEQTL>
+
+# Session Information
+
+```{r sessionInfo, eval=TRUE}
+sessionInfo()
+```