Nothing
inst/scripts/make-metadata_regulondb_sqlite.R
In regutools: regutools: an R package for data extraction from RegulonDB
library('here')
library('sessioninfo')
outdir <- 'regutools_files'
pkgname <- 'regutools'
meta <- data.frame(
Title = 'RegulonDB SQLite database version v10.6.2_DM for the regutools Bioconductor package',
Description = "An SQLite version of the RegulonDB database specifically tailored for the regutools Bioconductor package.",
BiocVersion = "3.10",
Genome = NA,
SourceType = "MySQL",
SourceUrl = 'https://bioconductor.org/packages/regutools',
SourceVersion = "Feb 25 2020",
Species = NA,
TaxonomyId = NA,
Coordinate_1_based = TRUE,
DataProvider = "RegulonDB",
Maintainer = "Leonardo Collado-Torres <lcolladotor@gmail.com>",
RDataClass = 'SQLite',
DispatchClass = 'SQLiteFile',
RDataPath = file.path(pkgname, outdir, 'regulon_sqlite3_v10.6.2_DM.db'),
Tags = 'regutools;RegulonDB;v10.6.2_DM',
row.names = NULL,
stringsAsFactors = FALSE
)
dir.create(here::here('inst', 'extdata'),
recursive = TRUE,
showWarnings = FALSE)
write.csv(
meta,
file = here::here('inst', 'extdata', 'metadata_regutools.csv'),
row.names = FALSE
)
## Check
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(here::here())
}
## 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
Try the regutools package in your browser
Any scripts or data that you put into this service are public.
regutools documentation built on Dec. 20, 2020, 2 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 <- 'regutools_files'
pkgname <- 'regutools'
meta <- data.frame(
Title = 'RegulonDB SQLite database version v10.6.2_DM for the regutools Bioconductor package',
Description = "An SQLite version of the RegulonDB database specifically tailored for the regutools Bioconductor package.",
BiocVersion = "3.10",
Genome = NA,
SourceType = "MySQL",
SourceUrl = 'https://bioconductor.org/packages/regutools',
SourceVersion = "Feb 25 2020",
Species = NA,
TaxonomyId = NA,
Coordinate_1_based = TRUE,
DataProvider = "RegulonDB",
Maintainer = "Leonardo Collado-Torres <lcolladotor@gmail.com>",
RDataClass = 'SQLite',
DispatchClass = 'SQLiteFile',
RDataPath = file.path(pkgname, outdir, 'regulon_sqlite3_v10.6.2_DM.db'),
Tags = 'regutools;RegulonDB;v10.6.2_DM',
row.names = NULL,
stringsAsFactors = FALSE
)
dir.create(here::here('inst', 'extdata'),
recursive = TRUE,
showWarnings = FALSE)
write.csv(
meta,
file = here::here('inst', 'extdata', 'metadata_regutools.csv'),
row.names = FALSE
)
## Check
if (FALSE) {
AnnotationHubData::makeAnnotationHubMetadata(here::here())
}
## 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
Try the regutools package in your browser
Any scripts or data that you put into this service are public.
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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