inst/scripts/make-metadata_GTEx_junctions.R
In dzhang32/dasper: Detecting abberant splicing events from RNA-sequencing data
library(sessioninfo)
library(stringr)
tissues <- c("fibroblast", "whole_blood", "skeletal_muscle", "lymphocytes", "skin_sun_exposed")
gtex_junctions_metadata <- data.frame(
Title = str_c("GTEx_v6_junctions_",
tissues),
Description = str_c(
"data.frame containing counts for all junctions originating from GTEx v6 ", str_replace_all(tissues, "_", " "), " samples.",
"Each row corresponds to a junction. Columns detail the 'chr', 'start', 'end', 'strand' and remaining columns refer to each GTEx sample in the format 'gtex_XXXXX', XXXXX being the rail_id from snaptron.",
"Data has been released via the recount2 project, downloaded by snaptron and wrangled into convienient format for use in the dasper package."
),
BiocVersion = "3.11",
Genome = "GRCh38",
SourceType = "TSV",
SourceUrl = "http://snaptron.cs.jhu.edu/",
SourceVersion = "Jul 20 2020",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "Genotype-Tissue Expression (GTEx) project - https://www.gtexportal.org/home/",
Maintainer = "David Zhang <dyzhang32@gmail.com>",
RDataClass = c("data.frame"),
DispatchClass = "Rda",
RDataPath = file.path("dasper",
str_c("GTEx_v6_junctions_",
tissues,
".rda")
),
Tags = "GTEx_v6_junctions",
row.names = NULL,
stringsAsFactors = FALSE
)
write.csv(gtex_junctions_metadata, file = "inst/extdata/metadata.csv", row.names = FALSE)
# check metadata format complies with Bioconductor guidelines
# AnnotationHubData::makeAnnotationHubMetadata(getwd())
## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.6.1 (2019-07-05)
# os Ubuntu 16.04.6 LTS
# system x86_64, linux-gnu
# ui RStudio
# language (EN)
# collate en_GB.UTF-8
# ctype en_GB.UTF-8
# tz Europe/London
# date 2020-07-20
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date lib source
# AnnotationDbi 1.46.1 2019-08-20 [2] Bioconductor
# AnnotationForge 1.26.0 2019-05-02 [1] Bioconductor
# AnnotationHub 2.16.1 2019-09-04 [1] Bioconductor
# AnnotationHubData 1.14.0 2019-05-02 [1] Bioconductor
# assertthat 0.2.1 2019-03-21 [2] CRAN (R 3.6.1)
# Biobase 2.44.0 2019-05-02 [2] Bioconductor
# BiocFileCache 1.8.0 2019-05-02 [1] Bioconductor
# BiocGenerics 0.30.0 2019-05-02 [2] Bioconductor
# BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.1)
# BiocParallel 1.18.1 2019-08-06 [1] Bioconductor
# biocViews 1.52.2 2019-05-29 [1] Bioconductor
# biomaRt 2.40.5 2019-10-01 [1] Bioconductor
# Biostrings 2.52.0 2019-05-02 [2] Bioconductor
# bit 1.1-14 2018-05-29 [2] CRAN (R 3.6.1)
# bit64 0.9-7 2017-05-08 [2] CRAN (R 3.6.1)
# bitops 1.0-6 2013-08-17 [2] CRAN (R 3.6.1)
# blob 1.2.0 2019-07-09 [2] CRAN (R 3.6.1)
# cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.1)
# crayon 1.3.4 2017-09-16 [2] CRAN (R 3.6.1)
# curl 4.3 2019-12-02 [1] CRAN (R 3.6.1)
# data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.1)
# DBI 1.1.0 2019-12-15 [2] CRAN (R 3.6.1)
# dbplyr 1.4.2 2019-06-17 [2] CRAN (R 3.6.1)
# DelayedArray 0.10.0 2019-05-02 [2] Bioconductor
# digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.1)
# dplyr 1.0.0 2020-05-29 [1] CRAN (R 3.6.1)
# ellipsis 0.3.1 2020-05-15 [1] CRAN (R 3.6.1)
# fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.1)
# fastmap 1.0.1 2019-10-08 [1] CRAN (R 3.6.1)
# formatR 1.7 2019-06-11 [2] CRAN (R 3.6.1)
# futile.logger * 1.4.3 2016-07-10 [2] CRAN (R 3.6.1)
# futile.options 1.0.1 2018-04-20 [2] CRAN (R 3.6.1)
# generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.1)
# GenomeInfoDb 1.20.0 2019-05-02 [1] Bioconductor
# GenomeInfoDbData 1.2.1 2019-09-21 [2] Bioconductor
# GenomicAlignments 1.20.1 2019-06-18 [2] Bioconductor
# GenomicFeatures 1.36.4 2019-07-10 [1] Bioconductor
# GenomicRanges 1.36.1 2019-09-06 [2] Bioconductor
# glue 1.4.1 2020-05-13 [1] CRAN (R 3.6.1)
# graph 1.62.0 2019-05-02 [1] Bioconductor
# hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.1)
# htmltools 0.5.0 2020-06-16 [1] CRAN (R 3.6.1)
# httpuv 1.5.2 2019-09-11 [2] CRAN (R 3.6.1)
# httr 1.4.1 2019-08-05 [2] CRAN (R 3.6.1)
# interactiveDisplayBase 1.22.0 2019-05-02 [1] Bioconductor
# IRanges 2.18.3 2019-09-24 [1] Bioconductor
# jsonlite 1.7.0 2020-06-25 [1] CRAN (R 3.6.1)
# lambda.r 1.2.4 2019-09-18 [2] CRAN (R 3.6.1)
# later 1.1.0.1 2020-06-05 [1] CRAN (R 3.6.1)
# lattice 0.20-38 2018-11-04 [4] CRAN (R 3.6.1)
# lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.1)
# magrittr 1.5 2014-11-22 [2] CRAN (R 3.6.1)
# Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.1)
# matrixStats 0.55.0 2019-09-07 [2] CRAN (R 3.6.1)
# memoise 1.1.0 2017-04-21 [2] CRAN (R 3.6.1)
# mime 0.9 2020-02-04 [1] CRAN (R 3.6.1)
# OrganismDbi 1.26.0 2019-05-02 [1] Bioconductor
# pillar 1.4.4 2020-05-05 [1] CRAN (R 3.6.1)
# pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 3.6.1)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.1)
# progress 1.2.2 2019-05-16 [2] CRAN (R 3.6.1)
# promises 1.1.1 2020-06-09 [1] CRAN (R 3.6.1)
# purrr 0.3.4 2020-04-17 [1] CRAN (R 3.6.1)
# R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
# rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.1)
# RBGL 1.60.0 2019-05-02 [1] Bioconductor
# rBiopaxParser 2.24.0 2019-05-02 [1] Bioconductor
# Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 3.6.1)
# RCurl 1.95-4.12 2019-03-04 [2] CRAN (R 3.6.1)
# rlang 0.4.6 2020-05-02 [1] CRAN (R 3.6.1)
# Rsamtools 2.0.3 2019-10-10 [1] Bioconductor
# RSQLite 2.1.2 2019-07-24 [2] CRAN (R 3.6.1)
# rstudioapi 0.11 2020-02-07 [2] CRAN (R 3.6.1)
# rtracklayer 1.44.4 2019-09-06 [2] Bioconductor
# RUnit 0.4.32 2018-05-18 [1] CRAN (R 3.6.1)
# S4Vectors 0.22.1 2019-09-09 [2] Bioconductor
# sessioninfo * 1.1.1 2018-11-05 [2] CRAN (R 3.6.1)
# shiny 1.5.0 2020-06-23 [1] CRAN (R 3.6.1)
# stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.1)
# stringr 1.4.0 2019-02-10 [2] CRAN (R 3.6.1)
# SummarizedExperiment 1.14.1 2019-07-31 [1] Bioconductor
# tibble 3.0.1 2020-04-20 [1] CRAN (R 3.6.1)
# tidyselect 1.1.0 2020-05-11 [1] CRAN (R 3.6.1)
# vctrs 0.3.1 2020-06-05 [1] CRAN (R 3.6.1)
# withr 2.2.0 2020-04-20 [1] CRAN (R 3.6.1)
# XML 3.99-0.3 2020-01-20 [2] CRAN (R 3.6.1)
# xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.1)
# XVector 0.24.0 2019-05-02 [2] Bioconductor
# yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.1)
# zlibbioc 1.30.0 2019-05-02 [2] Bioconductor
#
# [1] /home/dzhang/R/x86_64-pc-linux-gnu-library/3.6
# [2] /usr/local/lib/R/site-library
# [3] /usr/lib/R/site-library
# [4] /usr/lib/R/library
dzhang32/dasper documentation built on Dec. 14, 2024, 8:33 p.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(sessioninfo)
library(stringr)
tissues <- c("fibroblast", "whole_blood", "skeletal_muscle", "lymphocytes", "skin_sun_exposed")
gtex_junctions_metadata <- data.frame(
Title = str_c("GTEx_v6_junctions_",
tissues),
Description = str_c(
"data.frame containing counts for all junctions originating from GTEx v6 ", str_replace_all(tissues, "_", " "), " samples.",
"Each row corresponds to a junction. Columns detail the 'chr', 'start', 'end', 'strand' and remaining columns refer to each GTEx sample in the format 'gtex_XXXXX', XXXXX being the rail_id from snaptron.",
"Data has been released via the recount2 project, downloaded by snaptron and wrangled into convienient format for use in the dasper package."
),
BiocVersion = "3.11",
Genome = "GRCh38",
SourceType = "TSV",
SourceUrl = "http://snaptron.cs.jhu.edu/",
SourceVersion = "Jul 20 2020",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "Genotype-Tissue Expression (GTEx) project - https://www.gtexportal.org/home/",
Maintainer = "David Zhang <dyzhang32@gmail.com>",
RDataClass = c("data.frame"),
DispatchClass = "Rda",
RDataPath = file.path("dasper",
str_c("GTEx_v6_junctions_",
tissues,
".rda")
),
Tags = "GTEx_v6_junctions",
row.names = NULL,
stringsAsFactors = FALSE
)
write.csv(gtex_junctions_metadata, file = "inst/extdata/metadata.csv", row.names = FALSE)
# check metadata format complies with Bioconductor guidelines
# AnnotationHubData::makeAnnotationHubMetadata(getwd())
## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.6.1 (2019-07-05)
# os Ubuntu 16.04.6 LTS
# system x86_64, linux-gnu
# ui RStudio
# language (EN)
# collate en_GB.UTF-8
# ctype en_GB.UTF-8
# tz Europe/London
# date 2020-07-20
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date lib source
# AnnotationDbi 1.46.1 2019-08-20 [2] Bioconductor
# AnnotationForge 1.26.0 2019-05-02 [1] Bioconductor
# AnnotationHub 2.16.1 2019-09-04 [1] Bioconductor
# AnnotationHubData 1.14.0 2019-05-02 [1] Bioconductor
# assertthat 0.2.1 2019-03-21 [2] CRAN (R 3.6.1)
# Biobase 2.44.0 2019-05-02 [2] Bioconductor
# BiocFileCache 1.8.0 2019-05-02 [1] Bioconductor
# BiocGenerics 0.30.0 2019-05-02 [2] Bioconductor
# BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.1)
# BiocParallel 1.18.1 2019-08-06 [1] Bioconductor
# biocViews 1.52.2 2019-05-29 [1] Bioconductor
# biomaRt 2.40.5 2019-10-01 [1] Bioconductor
# Biostrings 2.52.0 2019-05-02 [2] Bioconductor
# bit 1.1-14 2018-05-29 [2] CRAN (R 3.6.1)
# bit64 0.9-7 2017-05-08 [2] CRAN (R 3.6.1)
# bitops 1.0-6 2013-08-17 [2] CRAN (R 3.6.1)
# blob 1.2.0 2019-07-09 [2] CRAN (R 3.6.1)
# cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.1)
# crayon 1.3.4 2017-09-16 [2] CRAN (R 3.6.1)
# curl 4.3 2019-12-02 [1] CRAN (R 3.6.1)
# data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.1)
# DBI 1.1.0 2019-12-15 [2] CRAN (R 3.6.1)
# dbplyr 1.4.2 2019-06-17 [2] CRAN (R 3.6.1)
# DelayedArray 0.10.0 2019-05-02 [2] Bioconductor
# digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.1)
# dplyr 1.0.0 2020-05-29 [1] CRAN (R 3.6.1)
# ellipsis 0.3.1 2020-05-15 [1] CRAN (R 3.6.1)
# fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.1)
# fastmap 1.0.1 2019-10-08 [1] CRAN (R 3.6.1)
# formatR 1.7 2019-06-11 [2] CRAN (R 3.6.1)
# futile.logger * 1.4.3 2016-07-10 [2] CRAN (R 3.6.1)
# futile.options 1.0.1 2018-04-20 [2] CRAN (R 3.6.1)
# generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.1)
# GenomeInfoDb 1.20.0 2019-05-02 [1] Bioconductor
# GenomeInfoDbData 1.2.1 2019-09-21 [2] Bioconductor
# GenomicAlignments 1.20.1 2019-06-18 [2] Bioconductor
# GenomicFeatures 1.36.4 2019-07-10 [1] Bioconductor
# GenomicRanges 1.36.1 2019-09-06 [2] Bioconductor
# glue 1.4.1 2020-05-13 [1] CRAN (R 3.6.1)
# graph 1.62.0 2019-05-02 [1] Bioconductor
# hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.1)
# htmltools 0.5.0 2020-06-16 [1] CRAN (R 3.6.1)
# httpuv 1.5.2 2019-09-11 [2] CRAN (R 3.6.1)
# httr 1.4.1 2019-08-05 [2] CRAN (R 3.6.1)
# interactiveDisplayBase 1.22.0 2019-05-02 [1] Bioconductor
# IRanges 2.18.3 2019-09-24 [1] Bioconductor
# jsonlite 1.7.0 2020-06-25 [1] CRAN (R 3.6.1)
# lambda.r 1.2.4 2019-09-18 [2] CRAN (R 3.6.1)
# later 1.1.0.1 2020-06-05 [1] CRAN (R 3.6.1)
# lattice 0.20-38 2018-11-04 [4] CRAN (R 3.6.1)
# lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.1)
# magrittr 1.5 2014-11-22 [2] CRAN (R 3.6.1)
# Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.1)
# matrixStats 0.55.0 2019-09-07 [2] CRAN (R 3.6.1)
# memoise 1.1.0 2017-04-21 [2] CRAN (R 3.6.1)
# mime 0.9 2020-02-04 [1] CRAN (R 3.6.1)
# OrganismDbi 1.26.0 2019-05-02 [1] Bioconductor
# pillar 1.4.4 2020-05-05 [1] CRAN (R 3.6.1)
# pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 3.6.1)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.1)
# progress 1.2.2 2019-05-16 [2] CRAN (R 3.6.1)
# promises 1.1.1 2020-06-09 [1] CRAN (R 3.6.1)
# purrr 0.3.4 2020-04-17 [1] CRAN (R 3.6.1)
# R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
# rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.1)
# RBGL 1.60.0 2019-05-02 [1] Bioconductor
# rBiopaxParser 2.24.0 2019-05-02 [1] Bioconductor
# Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 3.6.1)
# RCurl 1.95-4.12 2019-03-04 [2] CRAN (R 3.6.1)
# rlang 0.4.6 2020-05-02 [1] CRAN (R 3.6.1)
# Rsamtools 2.0.3 2019-10-10 [1] Bioconductor
# RSQLite 2.1.2 2019-07-24 [2] CRAN (R 3.6.1)
# rstudioapi 0.11 2020-02-07 [2] CRAN (R 3.6.1)
# rtracklayer 1.44.4 2019-09-06 [2] Bioconductor
# RUnit 0.4.32 2018-05-18 [1] CRAN (R 3.6.1)
# S4Vectors 0.22.1 2019-09-09 [2] Bioconductor
# sessioninfo * 1.1.1 2018-11-05 [2] CRAN (R 3.6.1)
# shiny 1.5.0 2020-06-23 [1] CRAN (R 3.6.1)
# stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.1)
# stringr 1.4.0 2019-02-10 [2] CRAN (R 3.6.1)
# SummarizedExperiment 1.14.1 2019-07-31 [1] Bioconductor
# tibble 3.0.1 2020-04-20 [1] CRAN (R 3.6.1)
# tidyselect 1.1.0 2020-05-11 [1] CRAN (R 3.6.1)
# vctrs 0.3.1 2020-06-05 [1] CRAN (R 3.6.1)
# withr 2.2.0 2020-04-20 [1] CRAN (R 3.6.1)
# XML 3.99-0.3 2020-01-20 [2] CRAN (R 3.6.1)
# xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.1)
# XVector 0.24.0 2019-05-02 [2] Bioconductor
# yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.1)
# zlibbioc 1.30.0 2019-05-02 [2] Bioconductor
#
# [1] /home/dzhang/R/x86_64-pc-linux-gnu-library/3.6
# [2] /usr/local/lib/R/site-library
# [3] /usr/lib/R/site-library
# [4] /usr/lib/R/library
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