| #' Retrieve temporary AWS authentication key, secret key and token | |
| #' | |
| #' Saturn Cloud instances use web authentication to obtain temporary | |
| #' access to AWS resources, e.g. S3 buckets, instead of environmental variables. | |
| #' But there are situations where the typical `AWS_ACCESS_KEY_ID`, | |
| #' `AWS_SECRET_ACCESS_KEY` and `AWS_SESSION_TOKEN` environmental variables are | |
| #' needed, e.g. to authenticate with tools that don't support web | |
| #' authentication such as the `aws.s3` and `paws` R packages. This function | |
| #' retrieves the temporary variables (but does not export them as environmental | |
| #' variables). |
| library(glue) | |
| library(purrr) | |
| library(rentrez) | |
| library(snakecase) | |
| library(tidyr) | |
| library(xml2) | |
| rentrez::entrez_dbs() # for reference: available databases | |
| # query NCBI GEO for information about Series GSE178265 |
| library(vcd) | |
| library(patchwork) | |
| set.seed(123) | |
| # we make 4 independent draws from a poisson | |
| # distribution, fit the poisson distribution | |
| # and then draw the rootogram to compare observed | |
| # and fitted values. | |
| plots <- lapply(1:4, function(draw) { |
| #' Retrieve Reactome sets of Entrez identifiers for a selected species | |
| #' | |
| #' @param species Scalar character, the species of interest, e.g. `Homo sapiens` | |
| #' @importFrom dplyr tbl right_join select collect mutate check_dbplyr | |
| #' @importFrom glue glue_sql glue | |
| #' @importFrom checkmate assert_choice | |
| #' @export | |
| #' @return A named list of Entrez identifiers | |
| #' @examples | |
| #' ReactomeSets("Mycobacterium tuberculosis") |
| library(limma) | |
| library(AnnotationDbi) | |
| library(GO.db) | |
| library(org.Hs.eg.db) | |
| # KEGG | |
| kegg.names <- getKEGGPathwayNames("hsa", remove.qualifier = TRUE) | |
| kegg.sets <- getGeneKEGGLinks("hsa", convert = TRUE) | |
| kegg.gsc <- with(kegg.sets, split(GeneID, PathwayID)) | |
| names(kegg.gsc) <- kegg.names[ |
| library(checkmate) | |
| library(dplyr) | |
| library(glue) | |
| library(htmltidy) | |
| library(httr) | |
| library(purrr) | |
| library(xml2) | |
| # https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html | |
| identify_accession_type <- function(accessions) { |
| library(DiagrammeR) # must be v 1.0.6.1 https://github.com/cynkra/dm/issues/823 | |
| library(dm) | |
| library(RSQLite) | |
| # download and decompress the chinook example SQLite database | |
| zip_file <- tempfile(fileext = ".zip") | |
| download.file( | |
| "https://www.sqlitetutorial.net/wp-content/uploads/2018/03/chinook.zip", | |
| destfile = zip_file) | |
| chinook <- unzip(zip_file, exdir = tempdir()) |
| library(BSgenome.Hsapiens.UCSC.hg38) | |
| library(Biostrings) | |
| library(Rsubread) | |
| library(GenomicRanges) | |
| library(parallel) | |
| library(GenomicAlignments) | |
| kCores <- parallel::detectCores() - 1L | |
| kQuery <- GRanges(seqnames = "chr12", IRanges(40263807, 40264221)) |
| libraries = c("zellkonverter", "SingleCellExperiment") | |
| for (lib in libraries) { | |
| suppressPackageStartupMessages(library(lib, character.only = TRUE, | |
| quietly = TRUE)) | |
| } | |
| # dummy SingleCellExperiment | |
| ncells <- 100 | |
| u <- matrix(rpois(20000, 5), ncol = ncells) | |
| v <- log2(u + 1) |