data-raw/create_spatialDLPFC_spe_subset.R
In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
library("spatialLIBD")
library("sessioninfo")
spe <- fetch_data("spatialDLPFC_Visium")
lobstr::obj_size(spe)
# 6.97 GB
## Subset to just 3 samples used in Figure 2A
spe <- spe[, spe$sample_id %in% c("Br8667_mid", "Br6522_ant", "Br6432_ant")]
lobstr::obj_size(spe)
# 777.93 MB
imgData(spe)
# DataFrame with 12 rows and 4 columns
# sample_id image_id data scaleFactor
# <character> <character> <list> <numeric>
# 1 Br6432_ant lowres #### 0.0148894
# 2 Br6432_ant hires #### 0.0496315
# 3 Br6432_ant detected #### 0.0496315
# 4 Br6432_ant aligned #### 0.0496315
# 5 Br6522_ant lowres #### 0.0192517
# ... ... ... ... ...
# 8 Br6522_ant aligned #### 0.0641725
# 9 Br8667_mid lowres #### 0.0169181
# 10 Br8667_mid hires #### 0.0563936
# 11 Br8667_mid detected #### 0.0563936
# 12 Br8667_mid aligned #### 0.0563936
## Subset to just the lowres images
imgData(spe) <- imgData(spe)[imgData(spe)$image_id == "lowres", ]
lobstr::obj_size(spe)
# 540.88 MB
saveRDS(spe, file = here::here("data-raw", "spatialDLPFC_spe_subset_example.rds"))
system2("ls", paste("-lh", here::here("data-raw", "spatialDLPFC_spe_subset_example.rds")))
# -rw-r--r--@ 1 leocollado staff 107M May 23 23:42 /Users/leocollado/Dropbox/Code/spatialLIBD/data-raw/spatialDLPFC_spe_subset_example.rds
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 4.3.0 (2023-04-21)
# os macOS Ventura 13.3.1
# system aarch64, darwin20
# ui RStudio
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz Europe/London
# date 2023-05-23
# rstudio 2023.03.1+446 Cherry Blossom (desktop)
# pandoc 2.17.1.1 @ /opt/homebrew/bin/pandoc
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date (UTC) lib source
# AnnotationDbi 1.62.1 2023-05-02 [1] Bioconductor
# AnnotationHub 3.8.0 2023-04-25 [1] Bioconductor
# attempt 0.3.1 2020-05-03 [1] CRAN (R 4.3.0)
# beachmat 2.16.0 2023-04-25 [1] Bioconductor
# beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.3.0)
# benchmarkme 1.0.8 2022-06-12 [1] CRAN (R 4.3.0)
# benchmarkmeData 1.0.4 2020-04-23 [1] CRAN (R 4.3.0)
# Biobase * 2.60.0 2023-04-25 [1] Bioconductor
# BiocFileCache 2.8.0 2023-04-25 [1] Bioconductor
# BiocGenerics * 0.46.0 2023-04-25 [1] Bioconductor
# BiocIO 1.10.0 2023-04-25 [1] Bioconductor
# BiocManager 1.30.20 2023-02-24 [1] CRAN (R 4.3.0)
# BiocNeighbors 1.18.0 2023-04-25 [1] Bioconductor
# BiocParallel 1.34.1 2023-05-08 [1] Bioconductor
# BiocSingular 1.16.0 2023-04-25 [1] Bioconductor
# biocthis 1.11.1 2023-05-06 [1] Github (lcolladotor/biocthis@42dc8df)
# BiocVersion 3.17.1 2022-12-20 [1] Bioconductor
# Biostrings 2.68.1 2023-05-16 [1] Bioconductor
# bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
# bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
# bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
# blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
# brio 1.1.3 2021-11-30 [1] CRAN (R 4.3.0)
# bslib 0.4.2 2022-12-16 [1] CRAN (R 4.3.0)
# cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
# callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
# cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
# codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.0)
# colorout 1.2-2 2023-05-06 [1] Github (jalvesaq/colorout@79931fd)
# colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
# config 0.3.1 2020-12-17 [1] CRAN (R 4.3.0)
# cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.3.0)
# crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
# curl 5.0.0 2023-01-12 [1] CRAN (R 4.3.0)
# data.table 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
# DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0)
# dbplyr 2.3.2 2023-03-21 [1] CRAN (R 4.3.0)
# DelayedArray 0.26.2 2023-05-05 [1] Bioconductor
# DelayedMatrixStats 1.22.0 2023-04-25 [1] Bioconductor
# devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
# digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0)
# doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.3.0)
# dotCall64 1.0-2 2022-10-03 [1] CRAN (R 4.3.0)
# dplyr 1.1.2 2023-04-20 [1] CRAN (R 4.3.0)
# dqrng 0.3.0 2021-05-01 [1] CRAN (R 4.3.0)
# DropletUtils 1.20.0 2023-05-08 [1] Bioconductor
# DT 0.28 2023-05-18 [1] CRAN (R 4.3.0)
# edgeR 3.42.2 2023-05-08 [1] Bioconductor
# ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
# ExperimentHub 2.8.0 2023-04-25 [1] Bioconductor
# fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
# fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
# fields 14.1 2022-08-12 [1] CRAN (R 4.3.0)
# filelock 1.0.2 2018-10-05 [1] CRAN (R 4.3.0)
# foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
# fs 1.6.2 2023-04-25 [1] CRAN (R 4.3.0)
# generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
# GenomeInfoDb * 1.36.0 2023-04-25 [1] Bioconductor
# GenomeInfoDbData 1.2.10 2023-05-06 [1] Bioconductor
# GenomicAlignments 1.36.0 2023-04-25 [1] Bioconductor
# GenomicRanges * 1.52.0 2023-04-25 [1] Bioconductor
# ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.3.0)
# ggplot2 3.4.2 2023-04-03 [1] CRAN (R 4.3.0)
# ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.3.0)
# glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
# golem 0.4.0 2023-03-12 [1] CRAN (R 4.3.0)
# gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.0)
# gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0)
# HDF5Array 1.28.1 2023-05-01 [1] Bioconductor
# here 1.0.1 2020-12-13 [1] CRAN (R 4.3.0)
# hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
# htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
# htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
# httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
# httr 1.4.6 2023-05-08 [1] CRAN (R 4.3.0)
# interactiveDisplayBase 1.38.0 2023-04-25 [1] Bioconductor
# IRanges * 2.34.0 2023-04-25 [1] Bioconductor
# irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.3.0)
# iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
# jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0)
# jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.3.0)
# KEGGREST 1.40.0 2023-04-25 [1] Bioconductor
# later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
# lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.0)
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# lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
# limma 3.56.1 2023-05-08 [1] Bioconductor
# lobstr 1.1.2 2022-06-22 [1] CRAN (R 4.3.0)
# locfit 1.5-9.7 2023-01-02 [1] CRAN (R 4.3.0)
# lubridate 1.9.2 2023-02-10 [1] CRAN (R 4.3.0)
# magick 2.7.4 2023-03-09 [1] CRAN (R 4.3.0)
# magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
# maps 3.4.1 2022-10-30 [1] CRAN (R 4.3.0)
# Matrix 1.5-4.1 2023-05-18 [1] CRAN (R 4.3.0)
# MatrixGenerics * 1.12.0 2023-04-25 [1] Bioconductor
# matrixStats * 0.63.0 2022-11-18 [1] CRAN (R 4.3.0)
# memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
# mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
# miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
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# pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.3.0)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
# pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.3.0)
# plotly 4.10.1 2022-11-07 [1] CRAN (R 4.3.0)
# png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.3.0)
# processx 3.8.1 2023-04-18 [1] CRAN (R 4.3.0)
# profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
# promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.3.0)
# prompt 1.0.1 2023-05-06 [1] Github (gaborcsardi/prompt@7ef0f2e)
# ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
# purrr 1.0.1 2023-01-10 [1] CRAN (R 4.3.0)
# R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.3.0)
# R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0)
# R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.0)
# R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.0)
# R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
# rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
# RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
# Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.3.0)
# RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
# rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.3.0)
# remotes 2.4.2 2021-11-30 [1] CRAN (R 4.3.0)
# restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
# rhdf5 2.44.0 2023-04-25 [1] Bioconductor
# rhdf5filters 1.12.1 2023-04-30 [1] Bioconductor
# Rhdf5lib 1.22.0 2023-04-25 [1] Bioconductor
# rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
# rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
# rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.3.0)
# Rsamtools 2.16.0 2023-04-25 [1] Bioconductor
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# rsthemes 0.4.0 2023-05-06 [1] Github (gadenbuie/rsthemes@34a55a4)
# rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0)
# rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.3.0)
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# S4Arrays 1.0.4 2023-05-14 [1] Bioconductor
# S4Vectors * 0.38.1 2023-05-02 [1] Bioconductor
# sass 0.4.6.9000 2023-05-06 [1] Github (rstudio/sass@f248fe5)
# ScaledMatrix 1.8.1 2023-05-03 [1] Bioconductor
# scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0)
# scater 1.28.0 2023-04-25 [1] Bioconductor
# scuttle 1.10.1 2023-05-02 [1] Bioconductor
# sessioninfo * 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
# shiny 1.7.4 2022-12-15 [1] CRAN (R 4.3.0)
# shinyWidgets 0.7.6 2023-01-08 [1] CRAN (R 4.3.0)
# SingleCellExperiment * 1.22.0 2023-04-25 [1] Bioconductor
# spam 2.9-1 2022-08-07 [1] CRAN (R 4.3.0)
# sparseMatrixStats 1.12.0 2023-04-25 [1] Bioconductor
# SpatialExperiment * 1.10.0 2023-04-25 [1] Bioconductor
# spatialLIBD * 1.12.0 2023-04-27 [1] Bioconductor
# statmod 1.5.0 2023-01-06 [1] CRAN (R 4.3.0)
# stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
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# zlibbioc 1.46.0 2023-04-25 [1] Bioconductor
#
# [1] /Library/Frameworks/R.framework/Versions/4.3-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("spatialLIBD")
library("sessioninfo")
spe <- fetch_data("spatialDLPFC_Visium")
lobstr::obj_size(spe)
# 6.97 GB
## Subset to just 3 samples used in Figure 2A
spe <- spe[, spe$sample_id %in% c("Br8667_mid", "Br6522_ant", "Br6432_ant")]
lobstr::obj_size(spe)
# 777.93 MB
imgData(spe)
# DataFrame with 12 rows and 4 columns
# sample_id image_id data scaleFactor
# <character> <character> <list> <numeric>
# 1 Br6432_ant lowres #### 0.0148894
# 2 Br6432_ant hires #### 0.0496315
# 3 Br6432_ant detected #### 0.0496315
# 4 Br6432_ant aligned #### 0.0496315
# 5 Br6522_ant lowres #### 0.0192517
# ... ... ... ... ...
# 8 Br6522_ant aligned #### 0.0641725
# 9 Br8667_mid lowres #### 0.0169181
# 10 Br8667_mid hires #### 0.0563936
# 11 Br8667_mid detected #### 0.0563936
# 12 Br8667_mid aligned #### 0.0563936
## Subset to just the lowres images
imgData(spe) <- imgData(spe)[imgData(spe)$image_id == "lowres", ]
lobstr::obj_size(spe)
# 540.88 MB
saveRDS(spe, file = here::here("data-raw", "spatialDLPFC_spe_subset_example.rds"))
system2("ls", paste("-lh", here::here("data-raw", "spatialDLPFC_spe_subset_example.rds")))
# -rw-r--r--@ 1 leocollado staff 107M May 23 23:42 /Users/leocollado/Dropbox/Code/spatialLIBD/data-raw/spatialDLPFC_spe_subset_example.rds
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 4.3.0 (2023-04-21)
# os macOS Ventura 13.3.1
# system aarch64, darwin20
# ui RStudio
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz Europe/London
# date 2023-05-23
# rstudio 2023.03.1+446 Cherry Blossom (desktop)
# pandoc 2.17.1.1 @ /opt/homebrew/bin/pandoc
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date (UTC) lib source
# AnnotationDbi 1.62.1 2023-05-02 [1] Bioconductor
# AnnotationHub 3.8.0 2023-04-25 [1] Bioconductor
# attempt 0.3.1 2020-05-03 [1] CRAN (R 4.3.0)
# beachmat 2.16.0 2023-04-25 [1] Bioconductor
# beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.3.0)
# benchmarkme 1.0.8 2022-06-12 [1] CRAN (R 4.3.0)
# benchmarkmeData 1.0.4 2020-04-23 [1] CRAN (R 4.3.0)
# Biobase * 2.60.0 2023-04-25 [1] Bioconductor
# BiocFileCache 2.8.0 2023-04-25 [1] Bioconductor
# BiocGenerics * 0.46.0 2023-04-25 [1] Bioconductor
# BiocIO 1.10.0 2023-04-25 [1] Bioconductor
# BiocManager 1.30.20 2023-02-24 [1] CRAN (R 4.3.0)
# BiocNeighbors 1.18.0 2023-04-25 [1] Bioconductor
# BiocParallel 1.34.1 2023-05-08 [1] Bioconductor
# BiocSingular 1.16.0 2023-04-25 [1] Bioconductor
# biocthis 1.11.1 2023-05-06 [1] Github (lcolladotor/biocthis@42dc8df)
# BiocVersion 3.17.1 2022-12-20 [1] Bioconductor
# Biostrings 2.68.1 2023-05-16 [1] Bioconductor
# bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
# bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
# bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
# blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
# brio 1.1.3 2021-11-30 [1] CRAN (R 4.3.0)
# bslib 0.4.2 2022-12-16 [1] CRAN (R 4.3.0)
# cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
# callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
# cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
# codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.0)
# colorout 1.2-2 2023-05-06 [1] Github (jalvesaq/colorout@79931fd)
# colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
# config 0.3.1 2020-12-17 [1] CRAN (R 4.3.0)
# cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.3.0)
# crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
# curl 5.0.0 2023-01-12 [1] CRAN (R 4.3.0)
# data.table 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
# DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0)
# dbplyr 2.3.2 2023-03-21 [1] CRAN (R 4.3.0)
# DelayedArray 0.26.2 2023-05-05 [1] Bioconductor
# DelayedMatrixStats 1.22.0 2023-04-25 [1] Bioconductor
# devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
# digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0)
# doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.3.0)
# dotCall64 1.0-2 2022-10-03 [1] CRAN (R 4.3.0)
# dplyr 1.1.2 2023-04-20 [1] CRAN (R 4.3.0)
# dqrng 0.3.0 2021-05-01 [1] CRAN (R 4.3.0)
# DropletUtils 1.20.0 2023-05-08 [1] Bioconductor
# DT 0.28 2023-05-18 [1] CRAN (R 4.3.0)
# edgeR 3.42.2 2023-05-08 [1] Bioconductor
# ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
# ExperimentHub 2.8.0 2023-04-25 [1] Bioconductor
# fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
# fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
# fields 14.1 2022-08-12 [1] CRAN (R 4.3.0)
# filelock 1.0.2 2018-10-05 [1] CRAN (R 4.3.0)
# foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
# fs 1.6.2 2023-04-25 [1] CRAN (R 4.3.0)
# generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
# GenomeInfoDb * 1.36.0 2023-04-25 [1] Bioconductor
# GenomeInfoDbData 1.2.10 2023-05-06 [1] Bioconductor
# GenomicAlignments 1.36.0 2023-04-25 [1] Bioconductor
# GenomicRanges * 1.52.0 2023-04-25 [1] Bioconductor
# ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.3.0)
# ggplot2 3.4.2 2023-04-03 [1] CRAN (R 4.3.0)
# ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.3.0)
# glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
# golem 0.4.0 2023-03-12 [1] CRAN (R 4.3.0)
# gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.0)
# gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0)
# HDF5Array 1.28.1 2023-05-01 [1] Bioconductor
# here 1.0.1 2020-12-13 [1] CRAN (R 4.3.0)
# hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
# htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
# htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
# httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
# httr 1.4.6 2023-05-08 [1] CRAN (R 4.3.0)
# interactiveDisplayBase 1.38.0 2023-04-25 [1] Bioconductor
# IRanges * 2.34.0 2023-04-25 [1] Bioconductor
# irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.3.0)
# iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
# jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0)
# jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.3.0)
# KEGGREST 1.40.0 2023-04-25 [1] Bioconductor
# later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
# lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.0)
# lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
# lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
# limma 3.56.1 2023-05-08 [1] Bioconductor
# lobstr 1.1.2 2022-06-22 [1] CRAN (R 4.3.0)
# locfit 1.5-9.7 2023-01-02 [1] CRAN (R 4.3.0)
# lubridate 1.9.2 2023-02-10 [1] CRAN (R 4.3.0)
# magick 2.7.4 2023-03-09 [1] CRAN (R 4.3.0)
# magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
# maps 3.4.1 2022-10-30 [1] CRAN (R 4.3.0)
# Matrix 1.5-4.1 2023-05-18 [1] CRAN (R 4.3.0)
# MatrixGenerics * 1.12.0 2023-04-25 [1] Bioconductor
# matrixStats * 0.63.0 2022-11-18 [1] CRAN (R 4.3.0)
# memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
# mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
# miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
# munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
# paletteer 1.5.0 2022-10-19 [1] CRAN (R 4.3.0)
# pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
# pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.3.0)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
# pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.3.0)
# plotly 4.10.1 2022-11-07 [1] CRAN (R 4.3.0)
# png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.3.0)
# processx 3.8.1 2023-04-18 [1] CRAN (R 4.3.0)
# profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
# promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.3.0)
# prompt 1.0.1 2023-05-06 [1] Github (gaborcsardi/prompt@7ef0f2e)
# ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
# purrr 1.0.1 2023-01-10 [1] CRAN (R 4.3.0)
# R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.3.0)
# R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0)
# R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.0)
# R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.0)
# R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
# rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
# RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
# Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.3.0)
# RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
# rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.3.0)
# remotes 2.4.2 2021-11-30 [1] CRAN (R 4.3.0)
# restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
# rhdf5 2.44.0 2023-04-25 [1] Bioconductor
# rhdf5filters 1.12.1 2023-04-30 [1] Bioconductor
# Rhdf5lib 1.22.0 2023-04-25 [1] Bioconductor
# rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
# rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
# rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.3.0)
# Rsamtools 2.16.0 2023-04-25 [1] Bioconductor
# RSQLite 2.3.1 2023-04-03 [1] CRAN (R 4.3.0)
# rsthemes 0.4.0 2023-05-06 [1] Github (gadenbuie/rsthemes@34a55a4)
# rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0)
# rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.3.0)
# rtracklayer 1.60.0 2023-04-25 [1] Bioconductor
# S4Arrays 1.0.4 2023-05-14 [1] Bioconductor
# S4Vectors * 0.38.1 2023-05-02 [1] Bioconductor
# sass 0.4.6.9000 2023-05-06 [1] Github (rstudio/sass@f248fe5)
# ScaledMatrix 1.8.1 2023-05-03 [1] Bioconductor
# scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0)
# scater 1.28.0 2023-04-25 [1] Bioconductor
# scuttle 1.10.1 2023-05-02 [1] Bioconductor
# sessioninfo * 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
# shiny 1.7.4 2022-12-15 [1] CRAN (R 4.3.0)
# shinyWidgets 0.7.6 2023-01-08 [1] CRAN (R 4.3.0)
# SingleCellExperiment * 1.22.0 2023-04-25 [1] Bioconductor
# spam 2.9-1 2022-08-07 [1] CRAN (R 4.3.0)
# sparseMatrixStats 1.12.0 2023-04-25 [1] Bioconductor
# SpatialExperiment * 1.10.0 2023-04-25 [1] Bioconductor
# spatialLIBD * 1.12.0 2023-04-27 [1] Bioconductor
# statmod 1.5.0 2023-01-06 [1] CRAN (R 4.3.0)
# stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
# stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.0)
# styler 1.9.1 2023-03-04 [1] CRAN (R 4.3.0)
# SummarizedExperiment * 1.30.1 2023-05-01 [1] Bioconductor
# suncalc 0.5.1 2022-09-29 [1] CRAN (R 4.3.0)
# testthat * 3.1.8 2023-05-04 [1] CRAN (R 4.3.0)
# tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
# tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.3.0)
# tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
# timechange 0.2.0 2023-01-11 [1] CRAN (R 4.3.0)
# urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
# usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.3.0)
# utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0)
# vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.3.0)
# vipor 0.4.5 2017-03-22 [1] CRAN (R 4.3.0)
# viridis 0.6.3 2023-05-03 [1] CRAN (R 4.3.0)
# viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
# withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.0)
# XML 3.99-0.14 2023-03-19 [1] CRAN (R 4.3.0)
# xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
# XVector 0.40.0 2023-04-25 [1] Bioconductor
# yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
# zlibbioc 1.46.0 2023-04-25 [1] Bioconductor
#
# [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#
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