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index.R
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index.R
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## ----install, eval = FALSE-------------------------------------------------
## ## For installing Bioconductor packages
## if (!requireNamespace("BiocManager", quietly = TRUE)) {
## install.packages("BiocManager")
## }
##
## ## Install required packages
## BiocManager::install(
## c(
## "usethis", ## Utilities
## "BiocFileCache",
## "RefManageR",
## "gitcreds",
## "gert",
## "gh",
## "here",
## "Hmisc",
## "biocthis",
## "lobstr",
## "postcards",
## "scater",
## "sessioninfo",
## "stringr",
## "SummarizedExperiment", ## Main containers / vis
## "iSEE",
## "edgeR", ## RNA-seq
## "ExploreModelMatrix",
## "limma",
## "smokingMouse",
## "recount3",
## "rlang",
## "scRNAseq",
## "airway",
## "pheatmap", ## Visualization
## "ggplot2",
## "ggrepel",
## "patchwork",
## "RColorBrewer",
## "ComplexHeatmap",
## "cowplot",
## "Polychrome",
## "spatialLIBD", ## Advanced
## "variancePartition"
## )
## )
## ----session_packages, eval = TRUE, message = FALSE------------------------
## Load the package at the top of your script
library("sessioninfo")
## Utilities
library("BiocFileCache")
library("BiocStyle")
library("biocthis")
library("gitcreds")
library("gert")
library("gh")
library("here")
library("lobstr")
library("postcards")
library("usethis")
library("sessioninfo")
## Data
library("smokingMouse")
library("scRNAseq")
## Main containers / vis
library("SummarizedExperiment")
library("iSEE")
## RNA-seq
library("airway")
library("edgeR")
library("ExploreModelMatrix")
library("limma")
library("recount3")
## QCA
library("scater")
## Variance Partition
library("variancePartition")
## Visualization: plots & text
library("ComplexHeatmap")
library("ggplot2")
library("patchwork")
library("pheatmap")
library("RColorBrewer")
library("Hmisc")
library("stringr")
library("cowplot")
library("rlang")
library("ggrepel")
library("Polychrome")
## Spatial transcriptomics
library("spatialLIBD")
## ----session_info----------------------------------------------------------
## Reproducibility information
options(width = 120)
session_info()
proc.time()
## ----"check_curl"----------------------------------------------------------
curl::curl_version()