inst/scripts/make-metadata_spatialLIBD.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(
"Human_Pilot_DLPFC_Visium_spatialLIBD_spot_level_SCE",
"Human_Pilot_DLPFC_Visium_spatialLIBD_layer_level_SCE",
"Human_Pilot_DLPFC_Visium_spatialLIBD_modeling_results",
"Human_DLPFC_Visium_sce_example"
),
Description = c(
"SingleCellExperiment object at the spot-level for the pilot human DLPFC spatial transcriptomics data from the Visium platform from 10x Genomics generated by the LIBD and available through the spatialLIBD Bioconductor package.",
"SingleCellExperiment object at the layer-level for the pilot human DLPFC spatial transcriptomics data from the Visium platform from 10x Genomics generated by the LIBD and available through the spatialLIBD Bioconductor package.",
"List of modeling results at the layer-level for the pilot human DLPFC spatial transcriptomics data from the Visium platform from 10x Genomics generated by the LIBD and available through the spatialLIBD Bioconductor package.",
"SingleCellExperiment object at the spot-level for the pilot human DLPFC spatial transcriptomics data from the Visium platform from 10x Genomics generated by the LIBD and available through the spatialLIBD Bioconductor package. It is a subset of the main object for example purposes."
),
BiocVersion = "3.10",
Genome = "GRCh38",
SourceType = "GTF",
SourceUrl = "https://bioconductor.org/packages/spatialLIBD",
SourceVersion = "Feb 19 2020",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "LIBD",
Maintainer = "Leonardo Collado-Torres <lcolladotor@gmail.com>",
RDataClass = c(
"SingleCellExperiment",
"SingleCellExperiment",
"list",
"SingleCellExperiment"
),
DispatchClass = "Rda",
RDataPath = file.path(
pkgname,
outdir,
c(
"Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata",
"Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata",
"Human_DLPFC_Visium_modeling_results.Rdata",
"sce_sub_for_vignette.Rdata"
)
),
Tags = "Human_Pilot_DLPFC_Visium_spatialLIBD",
row.names = NULL,
stringsAsFactors = FALSE
)
write.csv(
meta,
file = here::here("inst", "extdata", "metadata_spatialLIBD.csv"),
row.names = FALSE
)
## Check
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(here::here(), fileName = "metadata_spatialLIBD.csv")
}
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.6.2 (2019-12-12)
# os macOS Catalina 10.15.2
# system x86_64, darwin15.6.0
# ui AQUA
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz America/New_York
# date 2020-02-19
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date lib source
# AnnotationDbi 1.48.0 2019-10-29 [1] Bioconductor
# AnnotationForge 1.28.0 2019-10-29 [1] Bioconductor
# AnnotationHub * 2.18.0 2019-10-29 [1] Bioconductor
# AnnotationHubData * 1.16.0 2019-10-29 [1] Bioconductor
# askpass 1.1 2019-01-13 [1] CRAN (R 3.6.0)
# assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
# backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0)
# Biobase 2.46.0 2019-10-29 [1] Bioconductor
# BiocFileCache * 1.10.2 2019-11-08 [1] Bioconductor
# BiocGenerics * 0.32.0 2019-10-29 [1] Bioconductor
# BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.1)
# BiocParallel 1.20.1 2019-12-21 [1] Bioconductor
# BiocVersion 3.10.1 2019-06-06 [1] Bioconductor
# biocViews 1.54.0 2019-10-29 [1] Bioconductor
# biomaRt 2.42.0 2019-10-29 [1] Bioconductor
# Biostrings 2.54.0 2019-10-29 [1] Bioconductor
# bit 1.1-15.1 2020-01-14 [1] CRAN (R 3.6.0)
# bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.0)
# bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
# blob 1.2.1 2020-01-20 [1] CRAN (R 3.6.0)
# callr 3.4.1 2020-01-24 [1] CRAN (R 3.6.2)
# cli 2.0.1 2020-01-08 [1] CRAN (R 3.6.0)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
# curl 4.3 2019-12-02 [1] CRAN (R 3.6.0)
# data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.1)
# DBI 1.1.0 2019-12-15 [1] CRAN (R 3.6.0)
# dbplyr * 1.4.2 2019-06-17 [1] CRAN (R 3.6.0)
# DelayedArray 0.12.2 2020-01-06 [1] Bioconductor
# desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
# devtools * 2.2.1 2019-09-24 [1] CRAN (R 3.6.1)
# digest 0.6.23 2019-11-23 [1] CRAN (R 3.6.0)
# dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.0)
# ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.0)
# fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0)
# fastmap 1.0.1 2019-10-08 [1] CRAN (R 3.6.0)
# formatR 1.7 2019-06-11 [1] CRAN (R 3.6.0)
# fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
# futile.logger * 1.4.3 2016-07-10 [1] CRAN (R 3.6.0)
# futile.options 1.0.1 2018-04-20 [1] CRAN (R 3.6.0)
# GenomeInfoDb * 1.22.0 2019-10-29 [1] Bioconductor
# GenomeInfoDbData 1.2.2 2019-10-31 [1] Bioconductor
# GenomicAlignments 1.22.1 2019-11-12 [1] Bioconductor
# GenomicFeatures 1.38.1 2020-01-22 [1] Bioconductor
# GenomicRanges * 1.38.0 2019-10-29 [1] Bioconductor
# glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
# graph 1.64.0 2019-10-29 [1] Bioconductor
# here * 0.1 2017-05-28 [1] CRAN (R 3.6.0)
# hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.0)
# htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0)
# httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.0)
# httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0)
# interactiveDisplayBase 1.24.0 2019-10-29 [1] Bioconductor
# IRanges * 2.20.2 2020-01-13 [1] Bioconductor
# jsonlite 1.6 2018-12-07 [1] CRAN (R 3.6.0)
# lambda.r 1.2.4 2019-09-18 [1] CRAN (R 3.6.0)
# later 1.0.0 2019-10-04 [1] CRAN (R 3.6.0)
# lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.2)
# magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
# Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.2)
# matrixStats 0.55.0 2019-09-07 [1] CRAN (R 3.6.0)
# memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
# mime 0.8 2019-12-19 [1] CRAN (R 3.6.0)
# openssl 1.4.1 2019-07-18 [1] CRAN (R 3.6.0)
# OrganismDbi 1.28.0 2019-10-29 [1] Bioconductor
# pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0)
# pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
# pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.2)
# processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
# progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.0)
# promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.0)
# ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
# purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.0)
# R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
# rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.0)
# RBGL 1.62.1 2019-10-30 [1] Bioconductor
# rBiopaxParser 2.26.0 2019-10-29 [1] Bioconductor
# Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.0)
# RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 3.6.0)
# remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.0)
# rlang 0.4.3 2020-01-24 [1] CRAN (R 3.6.2)
# rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
# Rsamtools 2.2.1 2019-11-06 [1] Bioconductor
# RSQLite 2.2.0 2020-01-07 [1] CRAN (R 3.6.0)
# rtracklayer 1.46.0 2019-10-29 [1] Bioconductor
# RUnit 0.4.32 2018-05-18 [1] CRAN (R 3.6.0)
# S4Vectors * 0.24.3 2020-01-18 [1] Bioconductor
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
# shiny 1.4.0 2019-10-10 [1] CRAN (R 3.6.0)
# stringi 1.4.5 2020-01-11 [1] CRAN (R 3.6.0)
# stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
# SummarizedExperiment 1.16.1 2019-12-19 [1] Bioconductor
# testthat * 2.3.1 2019-12-01 [1] CRAN (R 3.6.0)
# tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
# tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
# usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
# vctrs 0.2.2 2020-01-24 [1] CRAN (R 3.6.2)
# withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
# XML 3.99-0.3 2020-01-20 [1] CRAN (R 3.6.0)
# xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.0)
# XVector 0.26.0 2019-10-29 [1] Bioconductor
# yaml 2.2.0 2018-07-25 [1] CRAN (R 3.6.0)
# zlibbioc 1.32.0 2019-10-29 [1] Bioconductor
#
# [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
LieberInstitute/spatialLIBD documentation built on Nov. 4, 2024, 11:57 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(
"Human_Pilot_DLPFC_Visium_spatialLIBD_spot_level_SCE",
"Human_Pilot_DLPFC_Visium_spatialLIBD_layer_level_SCE",
"Human_Pilot_DLPFC_Visium_spatialLIBD_modeling_results",
"Human_DLPFC_Visium_sce_example"
),
Description = c(
"SingleCellExperiment object at the spot-level for the pilot human DLPFC spatial transcriptomics data from the Visium platform from 10x Genomics generated by the LIBD and available through the spatialLIBD Bioconductor package.",
"SingleCellExperiment object at the layer-level for the pilot human DLPFC spatial transcriptomics data from the Visium platform from 10x Genomics generated by the LIBD and available through the spatialLIBD Bioconductor package.",
"List of modeling results at the layer-level for the pilot human DLPFC spatial transcriptomics data from the Visium platform from 10x Genomics generated by the LIBD and available through the spatialLIBD Bioconductor package.",
"SingleCellExperiment object at the spot-level for the pilot human DLPFC spatial transcriptomics data from the Visium platform from 10x Genomics generated by the LIBD and available through the spatialLIBD Bioconductor package. It is a subset of the main object for example purposes."
),
BiocVersion = "3.10",
Genome = "GRCh38",
SourceType = "GTF",
SourceUrl = "https://bioconductor.org/packages/spatialLIBD",
SourceVersion = "Feb 19 2020",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "LIBD",
Maintainer = "Leonardo Collado-Torres <lcolladotor@gmail.com>",
RDataClass = c(
"SingleCellExperiment",
"SingleCellExperiment",
"list",
"SingleCellExperiment"
),
DispatchClass = "Rda",
RDataPath = file.path(
pkgname,
outdir,
c(
"Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata",
"Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata",
"Human_DLPFC_Visium_modeling_results.Rdata",
"sce_sub_for_vignette.Rdata"
)
),
Tags = "Human_Pilot_DLPFC_Visium_spatialLIBD",
row.names = NULL,
stringsAsFactors = FALSE
)
write.csv(
meta,
file = here::here("inst", "extdata", "metadata_spatialLIBD.csv"),
row.names = FALSE
)
## Check
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(here::here(), fileName = "metadata_spatialLIBD.csv")
}
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.6.2 (2019-12-12)
# os macOS Catalina 10.15.2
# system x86_64, darwin15.6.0
# ui AQUA
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz America/New_York
# date 2020-02-19
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date lib source
# AnnotationDbi 1.48.0 2019-10-29 [1] Bioconductor
# AnnotationForge 1.28.0 2019-10-29 [1] Bioconductor
# AnnotationHub * 2.18.0 2019-10-29 [1] Bioconductor
# AnnotationHubData * 1.16.0 2019-10-29 [1] Bioconductor
# askpass 1.1 2019-01-13 [1] CRAN (R 3.6.0)
# assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
# backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0)
# Biobase 2.46.0 2019-10-29 [1] Bioconductor
# BiocFileCache * 1.10.2 2019-11-08 [1] Bioconductor
# BiocGenerics * 0.32.0 2019-10-29 [1] Bioconductor
# BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.1)
# BiocParallel 1.20.1 2019-12-21 [1] Bioconductor
# BiocVersion 3.10.1 2019-06-06 [1] Bioconductor
# biocViews 1.54.0 2019-10-29 [1] Bioconductor
# biomaRt 2.42.0 2019-10-29 [1] Bioconductor
# Biostrings 2.54.0 2019-10-29 [1] Bioconductor
# bit 1.1-15.1 2020-01-14 [1] CRAN (R 3.6.0)
# bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.0)
# bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
# blob 1.2.1 2020-01-20 [1] CRAN (R 3.6.0)
# callr 3.4.1 2020-01-24 [1] CRAN (R 3.6.2)
# cli 2.0.1 2020-01-08 [1] CRAN (R 3.6.0)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
# curl 4.3 2019-12-02 [1] CRAN (R 3.6.0)
# data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.1)
# DBI 1.1.0 2019-12-15 [1] CRAN (R 3.6.0)
# dbplyr * 1.4.2 2019-06-17 [1] CRAN (R 3.6.0)
# DelayedArray 0.12.2 2020-01-06 [1] Bioconductor
# desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
# devtools * 2.2.1 2019-09-24 [1] CRAN (R 3.6.1)
# digest 0.6.23 2019-11-23 [1] CRAN (R 3.6.0)
# dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.0)
# ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.0)
# fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0)
# fastmap 1.0.1 2019-10-08 [1] CRAN (R 3.6.0)
# formatR 1.7 2019-06-11 [1] CRAN (R 3.6.0)
# fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
# futile.logger * 1.4.3 2016-07-10 [1] CRAN (R 3.6.0)
# futile.options 1.0.1 2018-04-20 [1] CRAN (R 3.6.0)
# GenomeInfoDb * 1.22.0 2019-10-29 [1] Bioconductor
# GenomeInfoDbData 1.2.2 2019-10-31 [1] Bioconductor
# GenomicAlignments 1.22.1 2019-11-12 [1] Bioconductor
# GenomicFeatures 1.38.1 2020-01-22 [1] Bioconductor
# GenomicRanges * 1.38.0 2019-10-29 [1] Bioconductor
# glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
# graph 1.64.0 2019-10-29 [1] Bioconductor
# here * 0.1 2017-05-28 [1] CRAN (R 3.6.0)
# hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.0)
# htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0)
# httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.0)
# httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0)
# interactiveDisplayBase 1.24.0 2019-10-29 [1] Bioconductor
# IRanges * 2.20.2 2020-01-13 [1] Bioconductor
# jsonlite 1.6 2018-12-07 [1] CRAN (R 3.6.0)
# lambda.r 1.2.4 2019-09-18 [1] CRAN (R 3.6.0)
# later 1.0.0 2019-10-04 [1] CRAN (R 3.6.0)
# lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.2)
# magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
# Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.2)
# matrixStats 0.55.0 2019-09-07 [1] CRAN (R 3.6.0)
# memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
# mime 0.8 2019-12-19 [1] CRAN (R 3.6.0)
# openssl 1.4.1 2019-07-18 [1] CRAN (R 3.6.0)
# OrganismDbi 1.28.0 2019-10-29 [1] Bioconductor
# pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0)
# pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
# pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.2)
# processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
# progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.0)
# promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.0)
# ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
# purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.0)
# R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
# rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.0)
# RBGL 1.62.1 2019-10-30 [1] Bioconductor
# rBiopaxParser 2.26.0 2019-10-29 [1] Bioconductor
# Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.0)
# RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 3.6.0)
# remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.0)
# rlang 0.4.3 2020-01-24 [1] CRAN (R 3.6.2)
# rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
# Rsamtools 2.2.1 2019-11-06 [1] Bioconductor
# RSQLite 2.2.0 2020-01-07 [1] CRAN (R 3.6.0)
# rtracklayer 1.46.0 2019-10-29 [1] Bioconductor
# RUnit 0.4.32 2018-05-18 [1] CRAN (R 3.6.0)
# S4Vectors * 0.24.3 2020-01-18 [1] Bioconductor
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
# shiny 1.4.0 2019-10-10 [1] CRAN (R 3.6.0)
# stringi 1.4.5 2020-01-11 [1] CRAN (R 3.6.0)
# stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
# SummarizedExperiment 1.16.1 2019-12-19 [1] Bioconductor
# testthat * 2.3.1 2019-12-01 [1] CRAN (R 3.6.0)
# tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
# tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
# usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
# vctrs 0.2.2 2020-01-24 [1] CRAN (R 3.6.2)
# withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
# XML 3.99-0.3 2020-01-20 [1] CRAN (R 3.6.0)
# xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.0)
# XVector 0.26.0 2019-10-29 [1] Bioconductor
# yaml 2.2.0 2018-07-25 [1] CRAN (R 3.6.0)
# zlibbioc 1.32.0 2019-10-29 [1] Bioconductor
#
# [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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