inst/scripts/make-metadata_spatialDLPFC.R
In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
library("here")
library("sessioninfo")
outdir <- "spatialLIBD_files"
pkgname <- "spatialLIBD"
meta <- data.frame(
Title = c(
"spatialDLPFC_Visium_spe",
"spatialDLPFC_Visium_example_subset",
"spatialDLPFC_Visium_pseudobulk_spe",
"spatialDLPFC_Visium_modeling_results",
"spatialDLPFC_Visium_SPG",
"spatialDLPFC_snRNAseq"
),
Description = c(
"SpatialExperiment object at the spot-level for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"SpatialExperiment object at the spot-level for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Subsetted to just 3 samples with only the lowres images for example purposes.",
"Pseudo-bulked SingleCellExperiment object (SpatialExperiment object without spatial data) at the Sp09D spatial domain resolution for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"List of modeling results at the Sp09D spatial domain resolution for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"SpatialExperiment object at the spot-level for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 4) from the Visium Spatial Proteogenomics (Visium-SPG) platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"SingleCellExperiment object for the spatialDLPFC human brain (DLPFC) single nucleus transcriptomics data (snRNA-seq, n = 19) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package."
),
BiocVersion = "3.17",
Genome = "GRCh38",
SourceType = "GTF",
SourceUrl = "https://bioconductor.org/packages/spatialLIBD",
SourceVersion = "Mar 17 2023",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "LIBD",
Maintainer = "Leonardo Collado-Torres <lcolladotor@gmail.com>",
RDataClass = c(
"SpatialExperiment",
"SpatialExperiment",
"SpatialExperiment",
"list",
"SpatialExperiment",
"SingleCellExperiment"
),
DispatchClass = c("Rds", "Rds", "Rds", "Rda", "Rds", "FilePath"),
RDataPath = file.path(
pkgname,
outdir,
c(
"spe_filtered_final_with_clusters_and_deconvolution_results.rds",
"spatialDLPFC_spe_subset_example.rds",
"sce_pseudo_BayesSpace_k09.rds",
"modeling_results_BayesSpace_k09.Rdata",
"spe.rds",
"sce_DLPFC_annotated.zip"
)
),
Tags = "spatialDLPFC_Visium_VisiumSPG_snRNAseq_spatialLIBD",
row.names = NULL,
stringsAsFactors = FALSE
)
write.csv(
meta,
file = here::here("inst", "extdata", "metadata_spatialDLPFC.csv"),
row.names = FALSE
)
## Check
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(here::here(), fileName = "metadata_spatialDLPFC.csv")
}
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 4.2.2 (2022-10-31)
# os macOS Ventura 13.0.1
# system aarch64, darwin20
# ui RStudio
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz America/Mexico_City
# date 2023-02-13
# rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
# pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date (UTC) lib source
# AnnotationDbi 1.60.0 2022-11-01 [1] Bioconductor
# AnnotationForge 1.40.0 2022-11-01 [1] Bioconductor
# AnnotationHub 3.6.0 2022-11-01 [1] Bioconductor
# AnnotationHubData 1.28.0 2022-11-01 [1] Bioconductor
# assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
# Biobase 2.58.0 2022-11-01 [1] Bioconductor
# BiocCheck 1.34.2 2022-11-20 [1] Bioconductor
# BiocFileCache 2.6.0 2022-11-01 [1] Bioconductor
# BiocGenerics 0.44.0 2022-11-01 [1] Bioconductor
# BiocIO 1.8.0 2022-11-01 [1] Bioconductor
# BiocManager 1.30.19 2022-10-25 [1] CRAN (R 4.2.0)
# BiocParallel 1.32.5 2022-12-25 [1] Bioconductor
# BiocVersion 3.16.0 2022-09-20 [1] Bioconductor
# biocViews 1.66.2 2022-12-25 [1] Bioconductor
# biomaRt 2.54.0 2022-11-01 [1] Bioconductor
# Biostrings 2.66.0 2022-11-01 [1] Bioconductor
# bit 4.0.5 2022-11-15 [1] CRAN (R 4.2.2)
# bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0)
# bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
# blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
# brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0)
# cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
# callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.2)
# cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0)
# codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.0)
# colorout 1.2-2 2022-03-01 [1] Github (jalvesaq/colorout@79931fd)
# crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
# curl 5.0.0 2023-01-12 [1] CRAN (R 4.2.0)
# data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.0)
# DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
# dbplyr 2.3.0 2023-01-16 [1] CRAN (R 4.2.0)
# DelayedArray 0.24.0 2022-11-01 [1] Bioconductor
# devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
# digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0)
# dplyr 1.1.0 2023-01-29 [1] CRAN (R 4.2.0)
# ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
# evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0)
# fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
# fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
# filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0)
# formatR 1.14 2023-01-17 [1] CRAN (R 4.2.0)
# fs 1.6.0 2023-01-23 [1] CRAN (R 4.2.0)
# futile.logger * 1.4.3 2016-07-10 [1] CRAN (R 4.2.0)
# futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.2.0)
# generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
# GenomeInfoDb 1.34.9 2023-02-02 [1] Bioconductor
# GenomeInfoDbData 1.2.9 2022-11-02 [1] Bioconductor
# GenomicAlignments 1.34.0 2022-11-01 [1] Bioconductor
# GenomicFeatures 1.50.4 2023-01-25 [1] Bioconductor
# GenomicRanges 1.50.2 2022-12-18 [1] Bioconductor
# glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
# graph 1.76.0 2022-11-01 [1] Bioconductor
# here * 1.0.1 2020-12-13 [1] CRAN (R 4.2.0)
# hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
# htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.0)
# htmlwidgets 1.6.1 2023-01-07 [1] CRAN (R 4.2.0)
# httpuv 1.6.8 2023-01-12 [1] CRAN (R 4.2.0)
# httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.0)
# interactiveDisplayBase 1.36.0 2022-11-01 [1] Bioconductor
# IRanges 2.32.0 2022-11-01 [1] Bioconductor
# jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.0)
# KEGGREST 1.38.0 2022-11-01 [1] Bioconductor
# knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0)
# lambda.r 1.2.4 2019-09-18 [1] CRAN (R 4.2.0)
# later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
# lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.2)
# lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
# lubridate 1.9.1 2023-01-24 [1] CRAN (R 4.2.0)
# magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
# Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.0)
# MatrixGenerics 1.10.0 2022-11-01 [1] Bioconductor
# matrixStats 0.63.0 2022-11-18 [1] CRAN (R 4.2.0)
# memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
# mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
# miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
# OrganismDbi 1.40.0 2022-11-01 [1] Bioconductor
# pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
# pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.2)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
# pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.2)
# png 0.1-8 2022-11-29 [1] CRAN (R 4.2.0)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
# processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.0)
# profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.0)
# progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0)
# promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
# prompt 1.0.1 2022-03-01 [1] Github (gaborcsardi/prompt@7ef0f2e)
# ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.0)
# purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
# R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
# rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.2.0)
# RBGL 1.74.0 2022-11-01 [1] Bioconductor
# Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.0)
# RCurl 1.98-1.10 2023-01-27 [1] CRAN (R 4.2.0)
# remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
# restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.2.0)
# rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0)
# rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
# rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.0)
# rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
# Rsamtools 2.14.0 2022-11-01 [1] Bioconductor
# RSQLite 2.2.20 2022-12-22 [1] CRAN (R 4.2.2)
# rsthemes 0.3.1 2022-03-01 [1] Github (gadenbuie/rsthemes@bbe73ca)
# rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
# rtracklayer 1.58.0 2022-11-01 [1] Bioconductor
# RUnit 0.4.32 2018-05-18 [1] CRAN (R 4.2.0)
# S4Vectors 0.36.1 2022-12-07 [1] Bioconductor
# sessioninfo * 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
# shiny 1.7.4 2022-12-15 [1] CRAN (R 4.2.2)
# stringdist 0.9.10 2022-11-07 [1] CRAN (R 4.2.0)
# stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0)
# stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
# SummarizedExperiment 1.28.0 2022-11-01 [1] Bioconductor
# suncalc 0.5.1 2022-09-29 [1] CRAN (R 4.2.0)
# testthat * 3.1.6 2022-12-09 [1] CRAN (R 4.2.0)
# tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
# tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
# timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.0)
# urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
# usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
# utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
# vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0)
# xfun 0.37 2023-01-31 [1] CRAN (R 4.2.0)
# XML 3.99-0.13 2022-12-04 [1] CRAN (R 4.2.0)
# xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
# xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
# XVector 0.38.0 2022-11-01 [1] Bioconductor
# yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
# zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
#
# [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
#
# ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
LieberInstitute/spatialLIBD documentation built on May 12, 2024, 12:22 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library("here")
library("sessioninfo")
outdir <- "spatialLIBD_files"
pkgname <- "spatialLIBD"
meta <- data.frame(
Title = c(
"spatialDLPFC_Visium_spe",
"spatialDLPFC_Visium_example_subset",
"spatialDLPFC_Visium_pseudobulk_spe",
"spatialDLPFC_Visium_modeling_results",
"spatialDLPFC_Visium_SPG",
"spatialDLPFC_snRNAseq"
),
Description = c(
"SpatialExperiment object at the spot-level for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"SpatialExperiment object at the spot-level for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Subsetted to just 3 samples with only the lowres images for example purposes.",
"Pseudo-bulked SingleCellExperiment object (SpatialExperiment object without spatial data) at the Sp09D spatial domain resolution for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"List of modeling results at the Sp09D spatial domain resolution for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"SpatialExperiment object at the spot-level for the spatialDLPFC human brain (DLPFC) spatial transcriptomics data (n = 4) from the Visium Spatial Proteogenomics (Visium-SPG) platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"SingleCellExperiment object for the spatialDLPFC human brain (DLPFC) single nucleus transcriptomics data (snRNA-seq, n = 19) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package."
),
BiocVersion = "3.17",
Genome = "GRCh38",
SourceType = "GTF",
SourceUrl = "https://bioconductor.org/packages/spatialLIBD",
SourceVersion = "Mar 17 2023",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "LIBD",
Maintainer = "Leonardo Collado-Torres <lcolladotor@gmail.com>",
RDataClass = c(
"SpatialExperiment",
"SpatialExperiment",
"SpatialExperiment",
"list",
"SpatialExperiment",
"SingleCellExperiment"
),
DispatchClass = c("Rds", "Rds", "Rds", "Rda", "Rds", "FilePath"),
RDataPath = file.path(
pkgname,
outdir,
c(
"spe_filtered_final_with_clusters_and_deconvolution_results.rds",
"spatialDLPFC_spe_subset_example.rds",
"sce_pseudo_BayesSpace_k09.rds",
"modeling_results_BayesSpace_k09.Rdata",
"spe.rds",
"sce_DLPFC_annotated.zip"
)
),
Tags = "spatialDLPFC_Visium_VisiumSPG_snRNAseq_spatialLIBD",
row.names = NULL,
stringsAsFactors = FALSE
)
write.csv(
meta,
file = here::here("inst", "extdata", "metadata_spatialDLPFC.csv"),
row.names = FALSE
)
## Check
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(here::here(), fileName = "metadata_spatialDLPFC.csv")
}
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 4.2.2 (2022-10-31)
# os macOS Ventura 13.0.1
# system aarch64, darwin20
# ui RStudio
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz America/Mexico_City
# date 2023-02-13
# rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
# pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date (UTC) lib source
# AnnotationDbi 1.60.0 2022-11-01 [1] Bioconductor
# AnnotationForge 1.40.0 2022-11-01 [1] Bioconductor
# AnnotationHub 3.6.0 2022-11-01 [1] Bioconductor
# AnnotationHubData 1.28.0 2022-11-01 [1] Bioconductor
# assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
# Biobase 2.58.0 2022-11-01 [1] Bioconductor
# BiocCheck 1.34.2 2022-11-20 [1] Bioconductor
# BiocFileCache 2.6.0 2022-11-01 [1] Bioconductor
# BiocGenerics 0.44.0 2022-11-01 [1] Bioconductor
# BiocIO 1.8.0 2022-11-01 [1] Bioconductor
# BiocManager 1.30.19 2022-10-25 [1] CRAN (R 4.2.0)
# BiocParallel 1.32.5 2022-12-25 [1] Bioconductor
# BiocVersion 3.16.0 2022-09-20 [1] Bioconductor
# biocViews 1.66.2 2022-12-25 [1] Bioconductor
# biomaRt 2.54.0 2022-11-01 [1] Bioconductor
# Biostrings 2.66.0 2022-11-01 [1] Bioconductor
# bit 4.0.5 2022-11-15 [1] CRAN (R 4.2.2)
# bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0)
# bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
# blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
# brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0)
# cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
# callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.2)
# cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0)
# codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.0)
# colorout 1.2-2 2022-03-01 [1] Github (jalvesaq/colorout@79931fd)
# crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
# curl 5.0.0 2023-01-12 [1] CRAN (R 4.2.0)
# data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.0)
# DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
# dbplyr 2.3.0 2023-01-16 [1] CRAN (R 4.2.0)
# DelayedArray 0.24.0 2022-11-01 [1] Bioconductor
# devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
# digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0)
# dplyr 1.1.0 2023-01-29 [1] CRAN (R 4.2.0)
# ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
# evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0)
# fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
# fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
# filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0)
# formatR 1.14 2023-01-17 [1] CRAN (R 4.2.0)
# fs 1.6.0 2023-01-23 [1] CRAN (R 4.2.0)
# futile.logger * 1.4.3 2016-07-10 [1] CRAN (R 4.2.0)
# futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.2.0)
# generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
# GenomeInfoDb 1.34.9 2023-02-02 [1] Bioconductor
# GenomeInfoDbData 1.2.9 2022-11-02 [1] Bioconductor
# GenomicAlignments 1.34.0 2022-11-01 [1] Bioconductor
# GenomicFeatures 1.50.4 2023-01-25 [1] Bioconductor
# GenomicRanges 1.50.2 2022-12-18 [1] Bioconductor
# glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
# graph 1.76.0 2022-11-01 [1] Bioconductor
# here * 1.0.1 2020-12-13 [1] CRAN (R 4.2.0)
# hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
# htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.0)
# htmlwidgets 1.6.1 2023-01-07 [1] CRAN (R 4.2.0)
# httpuv 1.6.8 2023-01-12 [1] CRAN (R 4.2.0)
# httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.0)
# interactiveDisplayBase 1.36.0 2022-11-01 [1] Bioconductor
# IRanges 2.32.0 2022-11-01 [1] Bioconductor
# jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.0)
# KEGGREST 1.38.0 2022-11-01 [1] Bioconductor
# knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0)
# lambda.r 1.2.4 2019-09-18 [1] CRAN (R 4.2.0)
# later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
# lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.2)
# lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
# lubridate 1.9.1 2023-01-24 [1] CRAN (R 4.2.0)
# magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
# Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.0)
# MatrixGenerics 1.10.0 2022-11-01 [1] Bioconductor
# matrixStats 0.63.0 2022-11-18 [1] CRAN (R 4.2.0)
# memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
# mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
# miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
# OrganismDbi 1.40.0 2022-11-01 [1] Bioconductor
# pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
# pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.2)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
# pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.2)
# png 0.1-8 2022-11-29 [1] CRAN (R 4.2.0)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
# processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.0)
# profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.0)
# progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0)
# promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
# prompt 1.0.1 2022-03-01 [1] Github (gaborcsardi/prompt@7ef0f2e)
# ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.0)
# purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
# R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
# rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.2.0)
# RBGL 1.74.0 2022-11-01 [1] Bioconductor
# Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.0)
# RCurl 1.98-1.10 2023-01-27 [1] CRAN (R 4.2.0)
# remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
# restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.2.0)
# rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0)
# rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
# rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.0)
# rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
# Rsamtools 2.14.0 2022-11-01 [1] Bioconductor
# RSQLite 2.2.20 2022-12-22 [1] CRAN (R 4.2.2)
# rsthemes 0.3.1 2022-03-01 [1] Github (gadenbuie/rsthemes@bbe73ca)
# rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
# rtracklayer 1.58.0 2022-11-01 [1] Bioconductor
# RUnit 0.4.32 2018-05-18 [1] CRAN (R 4.2.0)
# S4Vectors 0.36.1 2022-12-07 [1] Bioconductor
# sessioninfo * 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
# shiny 1.7.4 2022-12-15 [1] CRAN (R 4.2.2)
# stringdist 0.9.10 2022-11-07 [1] CRAN (R 4.2.0)
# stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0)
# stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
# SummarizedExperiment 1.28.0 2022-11-01 [1] Bioconductor
# suncalc 0.5.1 2022-09-29 [1] CRAN (R 4.2.0)
# testthat * 3.1.6 2022-12-09 [1] CRAN (R 4.2.0)
# tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
# tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
# timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.0)
# urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
# usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
# utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
# vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0)
# xfun 0.37 2023-01-31 [1] CRAN (R 4.2.0)
# XML 3.99-0.13 2022-12-04 [1] CRAN (R 4.2.0)
# xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
# xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
# XVector 0.38.0 2022-11-01 [1] Bioconductor
# yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
# zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
#
# [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
#
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