Skip to content

Commit

Permalink
Add metadata and a script to generate it for the Visium LS data
Browse files Browse the repository at this point in the history
  • Loading branch information
@Nick-Eagles
Nick-Eagles committed Jun 11, 2024
1 parent 813bcac commit 3b6fbc5
Show file tree
Hide file tree
Showing 2 changed files with 187 additions and 0 deletions.
3 changes: 3 additions & 0 deletions inst/extdata/metadata_Visium_LS.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags
Visium_LS_spe,SpatialExperiment object at the spot-level for the spatially stitched lateral septum human brain (LS) 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.,3.19,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,SpatialExperiment,Rds,spatialLIBD/spatialLIBD_files/Visium_LS_spe.rds,VisiumLS_Visium_stitched_spatialLIBD
Visium_LS_spaceranger,Spaceranger outputs for the spatially stitched lateral septum human brain (LS) 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.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,list,Zip,spatialLIBD/spatialLIBD_files/Visium_LS_spaceranger.zip,VisiumLS_Visium_stitched_spatialLIBD
184 changes: 184 additions & 0 deletions inst/scripts/make-metadata_Visium_LS.R
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,184 @@
library(here)
library(sessioninfo)
library(tidyverse)

outdir <- "spatialLIBD_files"
pkgname <- "spatialLIBD"

meta = tibble(
Title = c("Visium_LS_spe", "Visium_LS_spaceranger"),
Description = c(
"SpatialExperiment object at the spot-level for the spatially stitched lateral septum human brain (LS) 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 lateral septum human brain (LS) 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."
),
BiocVersion = "3.19",
Genome = "GRCh38",
SourceType = c("GTF", "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 <[email protected]>",
RDataClass = c("SpatialExperiment", "list"),
DispatchClass = c("Rds", "Zip"),
RDataPath = file.path(
pkgname,
outdir,
c("Visium_LS_spe.rds", "Visium_LS_spaceranger.zip")
),
Tags = "VisiumLS_Visium_stitched_spatialLIBD"
)

write_csv(meta, here("inst", "extdata", "metadata_Visium_LS.csv"))

## Check interactively
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(
here(), fileName = "metadata_Visium_LS.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

# ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

0 comments on commit 3b6fbc5

Please sign in to comment.