Last updated: 2025-04-09

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Introduction

We estimated the parameters for the e+s+apa model in this analysis. The apa component follows the approach described in this study https://www.nature.com/articles/s41588-021-00864-5. For each gene, we used the lead QTL to construct a PredictDB model.

library(ctwas)
library(ggplot2)
library(tidyverse)

source("/project/xinhe/xsun/multi_group_ctwas/data/samplesize.R")


folder_results_susieST <- "/project/xinhe/xsun/multi_group_ctwas/16.apa_li_weights/snakemake_outputs/"

# mapping_predictdb <- readRDS("/project2/xinhe/shared_data/multigroup_ctwas/weights/mapping_files/PredictDB_mapping.RDS")
# mapping_munro <- readRDS("/project2/xinhe/shared_data/multigroup_ctwas/weights/mapping_files/Munro_mapping.RDS")
# mapping_two <- rbind(mapping_predictdb,mapping_munro)

colors <- c(  "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728",  "#9467bd", "#8c564b", "#e377c2", "#7f7f7f",  "#bcbd22",  "#17becf",  "#f7b6d2",  "#c5b0d5",  "#9edae5", "#ffbb78",  "#98df8a",  "#ff9896" )

plot_piechart <- function(ctwas_parameters, colors, by, title) {
  # Create the initial data frame
  data <- data.frame(
    category = names(ctwas_parameters$prop_heritability),
    percentage = ctwas_parameters$prop_heritability
  )
  
  # Split the category into context and type
  data <- data %>%
    mutate(
      context = sub("\\|.*", "", category),
      type = sub(".*\\|", "", category)
    )
  
  # Aggregate the data based on the 'by' parameter
  if (by == "type") {
    data <- data %>%
      group_by(type) %>%
      summarize(percentage = sum(percentage)) %>%
      mutate(category = type)  # Use type as the new category
  } else if (by == "context") {
    data <- data %>%
      group_by(context) %>%
      summarize(percentage = sum(percentage)) %>%
      mutate(category = context)  # Use context as the new category
  } else {
    stop("Invalid 'by' parameter. Use 'type' or 'context'.")
  }
  
  # Calculate percentage labels for the chart
  data$percentage_label <- paste0(round(data$percentage * 100, 1), "%")
  
  # Create the pie chart
  pie <- ggplot(data, aes(x = "", y = percentage, fill = category)) +
    geom_bar(stat = "identity", width = 1) +
    coord_polar("y", start = 0) +
    theme_void() +  # Remove background and axes
    geom_text(aes(label = percentage_label), 
              position = position_stack(vjust = 0.5), size = 3) +  # Adjust size as needed
    scale_fill_manual(values = colors) +  # Custom colors
    labs(fill = "Category") +  # Legend title
    ggtitle(title)  # Title
  
  return(pie)
}

LDL-ukb-d-30780_irnt

Setting: shared_all, thin = 0.1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

IBD-ebi-a-GCST004131

Setting: shared_all, thin = 0.1

trait <- "IBD-ebi-a-GCST004131"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

T2D-panukb

Setting: shared_all, thin = 0.1

trait <- "T2D-panukb"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

aFib-ebi-a-GCST006414

Setting: shared_all, thin = 0.1

trait <- "aFib-ebi-a-GCST006414"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_all, thin = 0.5

thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_all, thin = 1

thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 0.1

thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 0.5

thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST

Setting: shared_type, thin = 1

thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("top-apa - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))

pve_pie_by_type_susieST


sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.1    stringr_1.5.1    dplyr_1.1.4      purrr_1.0.2     
 [5] readr_2.1.2      tidyr_1.3.0      tibble_3.2.1     tidyverse_1.3.1 
 [9] ggplot2_3.5.1    ctwas_0.5.4.9000

loaded via a namespace (and not attached):
  [1] colorspace_2.0-3            rjson_0.2.21               
  [3] ellipsis_0.3.2              rprojroot_2.0.3            
  [5] XVector_0.36.0              locuszoomr_0.2.1           
  [7] GenomicRanges_1.48.0        base64enc_0.1-3            
  [9] fs_1.5.2                    rstudioapi_0.13            
 [11] farver_2.1.0                ggrepel_0.9.1              
 [13] bit64_4.0.5                 lubridate_1.8.0            
 [15] AnnotationDbi_1.58.0        fansi_1.0.3                
 [17] xml2_1.3.3                  codetools_0.2-18           
 [19] logging_0.10-108            cachem_1.0.6               
 [21] knitr_1.39                  jsonlite_1.8.0             
 [23] workflowr_1.7.0             Rsamtools_2.12.0           
 [25] broom_0.8.0                 dbplyr_2.1.1               
 [27] png_0.1-7                   compiler_4.2.0             
 [29] httr_1.4.3                  backports_1.4.1            
 [31] assertthat_0.2.1            Matrix_1.5-3               
 [33] fastmap_1.1.0               lazyeval_0.2.2             
 [35] cli_3.6.1                   later_1.3.0                
 [37] htmltools_0.5.2             prettyunits_1.1.1          
 [39] tools_4.2.0                 gtable_0.3.0               
 [41] glue_1.6.2                  GenomeInfoDbData_1.2.8     
 [43] rappdirs_0.3.3              Rcpp_1.0.12                
 [45] Biobase_2.56.0              cellranger_1.1.0           
 [47] jquerylib_0.1.4             vctrs_0.6.5                
 [49] Biostrings_2.64.0           rtracklayer_1.56.0         
 [51] xfun_0.41                   rvest_1.0.2                
 [53] irlba_2.3.5                 lifecycle_1.0.4            
 [55] restfulr_0.0.14             ensembldb_2.20.2           
 [57] XML_3.99-0.14               zlibbioc_1.42.0            
 [59] zoo_1.8-10                  scales_1.3.0               
 [61] gggrid_0.2-0                hms_1.1.1                  
 [63] promises_1.2.0.1            MatrixGenerics_1.8.0       
 [65] ProtGenerics_1.28.0         parallel_4.2.0             
 [67] SummarizedExperiment_1.26.1 AnnotationFilter_1.20.0    
 [69] LDlinkR_1.2.3               yaml_2.3.5                 
 [71] curl_4.3.2                  memoise_2.0.1              
 [73] sass_0.4.1                  biomaRt_2.54.1             
 [75] stringi_1.7.6               RSQLite_2.3.1              
 [77] highr_0.9                   S4Vectors_0.34.0           
 [79] BiocIO_1.6.0                GenomicFeatures_1.48.3     
 [81] BiocGenerics_0.42.0         filelock_1.0.2             
 [83] BiocParallel_1.30.3         repr_1.1.4                 
 [85] GenomeInfoDb_1.39.9         rlang_1.1.2                
 [87] pkgconfig_2.0.3             matrixStats_0.62.0         
 [89] bitops_1.0-7                evaluate_0.15              
 [91] lattice_0.20-45             labeling_0.4.2             
 [93] GenomicAlignments_1.32.0    htmlwidgets_1.5.4          
 [95] cowplot_1.1.1               bit_4.0.4                  
 [97] tidyselect_1.2.0            magrittr_2.0.3             
 [99] AMR_2.1.1                   R6_2.5.1                   
[101] IRanges_2.30.0              generics_0.1.2             
[103] DelayedArray_0.22.0         DBI_1.2.2                  
[105] haven_2.5.0                 withr_2.5.0                
[107] pgenlibr_0.3.3              pillar_1.9.0               
[109] KEGGREST_1.36.3             RCurl_1.98-1.7             
[111] mixsqp_0.3-43               modelr_0.1.8               
[113] crayon_1.5.1                utf8_1.2.2                 
[115] BiocFileCache_2.4.0         plotly_4.10.0              
[117] tzdb_0.4.0                  rmarkdown_2.25             
[119] progress_1.2.2              readxl_1.4.0               
[121] grid_4.2.0                  data.table_1.14.2          
[123] blob_1.2.3                  git2r_0.30.1               
[125] reprex_2.0.1                digest_0.6.29              
[127] httpuv_1.6.5                stats4_4.2.0               
[129] munsell_0.5.0               viridisLite_0.4.0          
[131] skimr_2.1.4                 bslib_0.3.1