inst/scripts/make-metadata_visiumStitched_brain.R
In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
library(here)
library(sessioninfo)
library(tidyverse)
outdir <- "spatialLIBD_files"
pkgname <- "spatialLIBD"
meta <- tibble(
Title = c("visiumStitched_brain_spe", "visiumStitched_brain_spaceranger", "visiumStitched_brain_Fiji_out"),
Description = c(
"SpatialExperiment object at the spot-level for the spatially stitched human brain spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"Spaceranger outputs for the spatially stitched human brain (spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.",
"Stitched PNG image and XML file from aligning human brain spatial transcriptomics data (n = 3) in Fiji. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package."
),
BiocVersion = "3.19",
Genome = "GRCh38",
SourceType = c("GTF", "Zip", "Zip"),
SourceUrl = "https://bioconductor.org/packages/spatialLIBD",
SourceVersion = "June 11 2024",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "LIBD",
Maintainer = "Leonardo Collado-Torres <lcolladotor@gmail.com>",
RDataClass = c("SpatialExperiment", "list", "list"),
DispatchClass = c("Rds", "Zip", "Zip"),
RDataPath = file.path(
pkgname,
outdir,
c(
"visiumStitched_brain_spe.rds", "visiumStitched_brain_spaceranger.zip",
"visiumStitched_brain_fiji_out.zip"
)
),
Tags = "visiumStitched_brain_spatialLIBD"
)
write_csv(meta, here("inst", "extdata", "metadata_visiumStitched_brain.csv"))
## Check interactively
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(
here(),
fileName = "metadata_visiumStitched_brain.csv"
)
}
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 4.4.0 Patched (2024-05-22 r86590)
# os Rocky Linux 9.2 (Blue Onyx)
# system x86_64, linux-gnu
# ui X11
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz US/Eastern
# date 2024-06-11
# pandoc 3.1.13 @ /jhpce/shared/community/core/conda_R/4.4/bin/pandoc
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date (UTC) lib source
# abind 1.4-5 2016-07-21 [2] CRAN (R 4.4.0)
# AnnotationDbi 1.66.0 2024-05-01 [2] Bioconductor 3.19 (R 4.4.0)
# AnnotationForge 1.46.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# AnnotationHub 3.12.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# AnnotationHubData 1.34.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
# Biobase 2.64.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocBaseUtils 1.6.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocCheck 1.40.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocFileCache 2.12.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocGenerics 0.50.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocIO 1.14.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocManager 1.30.23 2024-05-04 [2] CRAN (R 4.4.0)
# BiocParallel 1.38.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocVersion 3.19.1 2024-04-17 [2] Bioconductor 3.19 (R 4.4.0)
# biocViews 1.72.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# biomaRt 2.60.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# Biostrings 2.72.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# bit 4.0.5 2022-11-15 [2] CRAN (R 4.4.0)
# bit64 4.0.5 2020-08-30 [2] CRAN (R 4.4.0)
# bitops 1.0-7 2021-04-24 [2] CRAN (R 4.4.0)
# blob 1.2.4 2023-03-17 [2] CRAN (R 4.4.0)
# cachem 1.1.0 2024-05-16 [2] CRAN (R 4.4.0)
# cli 3.6.2 2023-12-11 [2] CRAN (R 4.4.0)
# codetools 0.2-20 2024-03-31 [3] CRAN (R 4.4.0)
# colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.4.0)
# crayon 1.5.2 2022-09-29 [2] CRAN (R 4.4.0)
# curl 5.2.1 2024-03-01 [2] CRAN (R 4.4.0)
# DBI 1.2.2 2024-02-16 [2] CRAN (R 4.4.0)
# dbplyr 2.5.0 2024-03-19 [2] CRAN (R 4.4.0)
# DelayedArray 0.30.1 2024-05-07 [2] Bioconductor 3.19 (R 4.4.0)
# digest 0.6.35 2024-03-11 [2] CRAN (R 4.4.0)
# dplyr * 1.1.4 2023-11-17 [2] CRAN (R 4.4.0)
# fansi 1.0.6 2023-12-08 [2] CRAN (R 4.4.0)
# fastmap 1.2.0 2024-05-15 [2] CRAN (R 4.4.0)
# filelock 1.0.3 2023-12-11 [2] CRAN (R 4.4.0)
# forcats * 1.0.0 2023-01-29 [2] CRAN (R 4.4.0)
# formatR 1.14 2023-01-17 [2] CRAN (R 4.4.0)
# futile.logger * 1.4.3 2016-07-10 [2] CRAN (R 4.4.0)
# futile.options 1.0.1 2018-04-20 [2] CRAN (R 4.4.0)
# generics 0.1.3 2022-07-05 [2] CRAN (R 4.4.0)
# GenomeInfoDb 1.40.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# GenomeInfoDbData 1.2.12 2024-05-23 [2] Bioconductor
# GenomicAlignments 1.40.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# GenomicFeatures 1.56.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# GenomicRanges 1.56.0 2024-05-01 [2] Bioconductor 3.19 (R 4.4.0)
# ggplot2 * 3.5.1 2024-04-23 [2] CRAN (R 4.4.0)
# glue 1.7.0 2024-01-09 [2] CRAN (R 4.4.0)
# graph 1.82.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# gtable 0.3.5 2024-04-22 [2] CRAN (R 4.4.0)
# here * 1.0.1 2020-12-13 [2] CRAN (R 4.4.0)
# hms 1.1.3 2023-03-21 [2] CRAN (R 4.4.0)
# httr 1.4.7 2023-08-15 [2] CRAN (R 4.4.0)
# httr2 1.0.1 2024-04-01 [2] CRAN (R 4.4.0)
# IRanges 2.38.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# jsonlite 1.8.8 2023-12-04 [2] CRAN (R 4.4.0)
# KEGGREST 1.44.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# knitr 1.46 2024-04-06 [2] CRAN (R 4.4.0)
# lambda.r 1.2.4 2019-09-18 [2] CRAN (R 4.4.0)
# lattice 0.22-6 2024-03-20 [3] CRAN (R 4.4.0)
# lifecycle 1.0.4 2023-11-07 [2] CRAN (R 4.4.0)
# lubridate * 1.9.3 2023-09-27 [2] CRAN (R 4.4.0)
# magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.4.0)
# Matrix 1.7-0 2024-04-26 [3] CRAN (R 4.4.0)
# MatrixGenerics 1.16.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# matrixStats 1.3.0 2024-04-11 [2] CRAN (R 4.4.0)
# memoise 2.0.1 2021-11-26 [2] CRAN (R 4.4.0)
# munsell 0.5.1 2024-04-01 [2] CRAN (R 4.4.0)
# OrganismDbi 1.46.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# pillar 1.9.0 2023-03-22 [2] CRAN (R 4.4.0)
# pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.4.0)
# png 0.1-8 2022-11-29 [2] CRAN (R 4.4.0)
# prettyunits 1.2.0 2023-09-24 [2] CRAN (R 4.4.0)
# progress 1.2.3 2023-12-06 [2] CRAN (R 4.4.0)
# purrr * 1.0.2 2023-08-10 [2] CRAN (R 4.4.0)
# R6 2.5.1 2021-08-19 [2] CRAN (R 4.4.0)
# rappdirs 0.3.3 2021-01-31 [2] CRAN (R 4.4.0)
# RBGL 1.80.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# RCurl 1.98-1.14 2024-01-09 [2] CRAN (R 4.4.0)
# readr * 2.1.5 2024-01-10 [2] CRAN (R 4.4.0)
# restfulr 0.0.15 2022-06-16 [2] CRAN (R 4.4.0)
# rjson 0.2.21 2022-01-09 [2] CRAN (R 4.4.0)
# rlang 1.1.3 2024-01-10 [2] CRAN (R 4.4.0)
# rprojroot 2.0.4 2023-11-05 [2] CRAN (R 4.4.0)
# Rsamtools 2.20.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# RSQLite 2.3.6 2024-03-31 [2] CRAN (R 4.4.0)
# rtracklayer 1.64.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# RUnit 0.4.33 2024-02-22 [2] CRAN (R 4.4.0)
# S4Arrays 1.4.1 2024-05-20 [2] Bioconductor 3.19 (R 4.4.0)
# S4Vectors 0.42.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# scales 1.3.0 2023-11-28 [2] CRAN (R 4.4.0)
# sessioninfo * 1.2.2 2021-12-06 [2] CRAN (R 4.4.0)
# SparseArray 1.4.5 2024-05-20 [2] Bioconductor 3.19 (R 4.4.0)
# stringdist 0.9.12 2023-11-28 [2] CRAN (R 4.4.0)
# stringi 1.8.4 2024-05-06 [2] CRAN (R 4.4.0)
# stringr * 1.5.1 2023-11-14 [2] CRAN (R 4.4.0)
# SummarizedExperiment 1.34.0 2024-05-01 [2] Bioconductor 3.19 (R 4.4.0)
# tibble * 3.2.1 2023-03-20 [2] CRAN (R 4.4.0)
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# XVector 0.44.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# yaml 2.3.8 2023-12-11 [2] CRAN (R 4.4.0)
# zlibbioc 1.50.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# [1] /users/neagles/R/4.4
# [2] /jhpce/shared/community/core/conda_R/4.4/R/lib64/R/site-library
# [3] /jhpce/shared/community/core/conda_R/4.4/R/lib64/R/library
# ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
LieberInstitute/spatialLIBD documentation built on Nov. 4, 2024, 11:57 a.m.
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library(here)
library(sessioninfo)
library(tidyverse)
outdir <- "spatialLIBD_files"
pkgname <- "spatialLIBD"
meta <- tibble(
Title = c("visiumStitched_brain_spe", "visiumStitched_brain_spaceranger", "visiumStitched_brain_Fiji_out"),
Description = c(
"SpatialExperiment object at the spot-level for the spatially stitched human brain spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
"Spaceranger outputs for the spatially stitched human brain (spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.",
"Stitched PNG image and XML file from aligning human brain spatial transcriptomics data (n = 3) in Fiji. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package."
),
BiocVersion = "3.19",
Genome = "GRCh38",
SourceType = c("GTF", "Zip", "Zip"),
SourceUrl = "https://bioconductor.org/packages/spatialLIBD",
SourceVersion = "June 11 2024",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "LIBD",
Maintainer = "Leonardo Collado-Torres <lcolladotor@gmail.com>",
RDataClass = c("SpatialExperiment", "list", "list"),
DispatchClass = c("Rds", "Zip", "Zip"),
RDataPath = file.path(
pkgname,
outdir,
c(
"visiumStitched_brain_spe.rds", "visiumStitched_brain_spaceranger.zip",
"visiumStitched_brain_fiji_out.zip"
)
),
Tags = "visiumStitched_brain_spatialLIBD"
)
write_csv(meta, here("inst", "extdata", "metadata_visiumStitched_brain.csv"))
## Check interactively
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(
here(),
fileName = "metadata_visiumStitched_brain.csv"
)
}
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 4.4.0 Patched (2024-05-22 r86590)
# os Rocky Linux 9.2 (Blue Onyx)
# system x86_64, linux-gnu
# ui X11
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz US/Eastern
# date 2024-06-11
# pandoc 3.1.13 @ /jhpce/shared/community/core/conda_R/4.4/bin/pandoc
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date (UTC) lib source
# abind 1.4-5 2016-07-21 [2] CRAN (R 4.4.0)
# AnnotationDbi 1.66.0 2024-05-01 [2] Bioconductor 3.19 (R 4.4.0)
# AnnotationForge 1.46.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# AnnotationHub 3.12.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# AnnotationHubData 1.34.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
# Biobase 2.64.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocBaseUtils 1.6.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocCheck 1.40.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocFileCache 2.12.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocGenerics 0.50.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocIO 1.14.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocManager 1.30.23 2024-05-04 [2] CRAN (R 4.4.0)
# BiocParallel 1.38.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# BiocVersion 3.19.1 2024-04-17 [2] Bioconductor 3.19 (R 4.4.0)
# biocViews 1.72.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# biomaRt 2.60.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# Biostrings 2.72.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# bit 4.0.5 2022-11-15 [2] CRAN (R 4.4.0)
# bit64 4.0.5 2020-08-30 [2] CRAN (R 4.4.0)
# bitops 1.0-7 2021-04-24 [2] CRAN (R 4.4.0)
# blob 1.2.4 2023-03-17 [2] CRAN (R 4.4.0)
# cachem 1.1.0 2024-05-16 [2] CRAN (R 4.4.0)
# cli 3.6.2 2023-12-11 [2] CRAN (R 4.4.0)
# codetools 0.2-20 2024-03-31 [3] CRAN (R 4.4.0)
# colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.4.0)
# crayon 1.5.2 2022-09-29 [2] CRAN (R 4.4.0)
# curl 5.2.1 2024-03-01 [2] CRAN (R 4.4.0)
# DBI 1.2.2 2024-02-16 [2] CRAN (R 4.4.0)
# dbplyr 2.5.0 2024-03-19 [2] CRAN (R 4.4.0)
# DelayedArray 0.30.1 2024-05-07 [2] Bioconductor 3.19 (R 4.4.0)
# digest 0.6.35 2024-03-11 [2] CRAN (R 4.4.0)
# dplyr * 1.1.4 2023-11-17 [2] CRAN (R 4.4.0)
# fansi 1.0.6 2023-12-08 [2] CRAN (R 4.4.0)
# fastmap 1.2.0 2024-05-15 [2] CRAN (R 4.4.0)
# filelock 1.0.3 2023-12-11 [2] CRAN (R 4.4.0)
# forcats * 1.0.0 2023-01-29 [2] CRAN (R 4.4.0)
# formatR 1.14 2023-01-17 [2] CRAN (R 4.4.0)
# futile.logger * 1.4.3 2016-07-10 [2] CRAN (R 4.4.0)
# futile.options 1.0.1 2018-04-20 [2] CRAN (R 4.4.0)
# generics 0.1.3 2022-07-05 [2] CRAN (R 4.4.0)
# GenomeInfoDb 1.40.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# GenomeInfoDbData 1.2.12 2024-05-23 [2] Bioconductor
# GenomicAlignments 1.40.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# GenomicFeatures 1.56.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# GenomicRanges 1.56.0 2024-05-01 [2] Bioconductor 3.19 (R 4.4.0)
# ggplot2 * 3.5.1 2024-04-23 [2] CRAN (R 4.4.0)
# glue 1.7.0 2024-01-09 [2] CRAN (R 4.4.0)
# graph 1.82.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# gtable 0.3.5 2024-04-22 [2] CRAN (R 4.4.0)
# here * 1.0.1 2020-12-13 [2] CRAN (R 4.4.0)
# hms 1.1.3 2023-03-21 [2] CRAN (R 4.4.0)
# httr 1.4.7 2023-08-15 [2] CRAN (R 4.4.0)
# httr2 1.0.1 2024-04-01 [2] CRAN (R 4.4.0)
# IRanges 2.38.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# jsonlite 1.8.8 2023-12-04 [2] CRAN (R 4.4.0)
# KEGGREST 1.44.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# knitr 1.46 2024-04-06 [2] CRAN (R 4.4.0)
# lambda.r 1.2.4 2019-09-18 [2] CRAN (R 4.4.0)
# lattice 0.22-6 2024-03-20 [3] CRAN (R 4.4.0)
# lifecycle 1.0.4 2023-11-07 [2] CRAN (R 4.4.0)
# lubridate * 1.9.3 2023-09-27 [2] CRAN (R 4.4.0)
# magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.4.0)
# Matrix 1.7-0 2024-04-26 [3] CRAN (R 4.4.0)
# MatrixGenerics 1.16.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# matrixStats 1.3.0 2024-04-11 [2] CRAN (R 4.4.0)
# memoise 2.0.1 2021-11-26 [2] CRAN (R 4.4.0)
# munsell 0.5.1 2024-04-01 [2] CRAN (R 4.4.0)
# OrganismDbi 1.46.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# pillar 1.9.0 2023-03-22 [2] CRAN (R 4.4.0)
# pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.4.0)
# png 0.1-8 2022-11-29 [2] CRAN (R 4.4.0)
# prettyunits 1.2.0 2023-09-24 [2] CRAN (R 4.4.0)
# progress 1.2.3 2023-12-06 [2] CRAN (R 4.4.0)
# purrr * 1.0.2 2023-08-10 [2] CRAN (R 4.4.0)
# R6 2.5.1 2021-08-19 [2] CRAN (R 4.4.0)
# rappdirs 0.3.3 2021-01-31 [2] CRAN (R 4.4.0)
# RBGL 1.80.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# RCurl 1.98-1.14 2024-01-09 [2] CRAN (R 4.4.0)
# readr * 2.1.5 2024-01-10 [2] CRAN (R 4.4.0)
# restfulr 0.0.15 2022-06-16 [2] CRAN (R 4.4.0)
# rjson 0.2.21 2022-01-09 [2] CRAN (R 4.4.0)
# rlang 1.1.3 2024-01-10 [2] CRAN (R 4.4.0)
# rprojroot 2.0.4 2023-11-05 [2] CRAN (R 4.4.0)
# Rsamtools 2.20.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# RSQLite 2.3.6 2024-03-31 [2] CRAN (R 4.4.0)
# rtracklayer 1.64.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# RUnit 0.4.33 2024-02-22 [2] CRAN (R 4.4.0)
# S4Arrays 1.4.1 2024-05-20 [2] Bioconductor 3.19 (R 4.4.0)
# S4Vectors 0.42.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# scales 1.3.0 2023-11-28 [2] CRAN (R 4.4.0)
# sessioninfo * 1.2.2 2021-12-06 [2] CRAN (R 4.4.0)
# SparseArray 1.4.5 2024-05-20 [2] Bioconductor 3.19 (R 4.4.0)
# stringdist 0.9.12 2023-11-28 [2] CRAN (R 4.4.0)
# stringi 1.8.4 2024-05-06 [2] CRAN (R 4.4.0)
# stringr * 1.5.1 2023-11-14 [2] CRAN (R 4.4.0)
# SummarizedExperiment 1.34.0 2024-05-01 [2] Bioconductor 3.19 (R 4.4.0)
# tibble * 3.2.1 2023-03-20 [2] CRAN (R 4.4.0)
# tidyr * 1.3.1 2024-01-24 [2] CRAN (R 4.4.0)
# tidyselect 1.2.1 2024-03-11 [2] CRAN (R 4.4.0)
# tidyverse * 2.0.0 2023-02-22 [2] CRAN (R 4.4.0)
# timechange 0.3.0 2024-01-18 [2] CRAN (R 4.4.0)
# txdbmaker 1.0.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# tzdb 0.4.0 2023-05-12 [2] CRAN (R 4.4.0)
# UCSC.utils 1.0.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# utf8 1.2.4 2023-10-22 [2] CRAN (R 4.4.0)
# vctrs 0.6.5 2023-12-01 [2] CRAN (R 4.4.0)
# vroom 1.6.5 2023-12-05 [2] CRAN (R 4.4.0)
# withr 3.0.0 2024-01-16 [2] CRAN (R 4.4.0)
# xfun 0.44 2024-05-15 [2] CRAN (R 4.4.0)
# XML 3.99-0.16.1 2024-01-22 [2] CRAN (R 4.4.0)
# xml2 1.3.6 2023-12-04 [2] CRAN (R 4.4.0)
# XVector 0.44.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# yaml 2.3.8 2023-12-11 [2] CRAN (R 4.4.0)
# zlibbioc 1.50.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
# [1] /users/neagles/R/4.4
# [2] /jhpce/shared/community/core/conda_R/4.4/R/lib64/R/site-library
# [3] /jhpce/shared/community/core/conda_R/4.4/R/lib64/R/library
# ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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