| library(splines) | |
| library(DESeq2) | |
| # make some demo data | |
| dds <- makeExampleDESeqDataSet(n=100, m=40) | |
| dds$condition <- sort(runif(40)) | |
| # make one gene where expression has a curve shape (just for demo) | |
| s_shape <- round(500 * sin(dds$condition*2*pi) + 1000 + rnorm(40,0,50)) | |
| mode(s_shape) <- "integer" | |
| counts(dds)[1,] <- s_shape |
| # Function to run to check if you have any missing `\value{}` tags | |
| check_missing_value <- function(pkg = ".") { | |
| pkg_root <- rprojroot::find_package_root_file(path = pkg) | |
| # find exported functions | |
| ns <- readLines(file.path(pkg_root, "NAMESPACE")) | |
| exports <- ns[which(grepl("export", ns))] | |
| # https://stackoverflow.com/questions/8613237/extract-info-inside-all-parenthesis-in-r | |
| exported_fxs <- stringr::str_extract(exports, "(?<=\\().+?(?=\\))") | |
| # parse all man pages |
| // save to windows-user directory | |
| linters: with_defaults(object_name_linter = NULL, | |
| object_length_linter(50), | |
| commented_code_linter = NULL, | |
| object_usage_linter = NULL, | |
| line_length_linter(120), | |
| cyclocomp_linter = cyclocomp_linter(50)) |
| format = """ | |
| [\uE0B6](fg:#1C4961)[$directory](bg:#1C4961)[\uE0B0](fg:#1C4961 bg:#2F79A1)$git_branch[\uE0B0](fg:#2F79A1 bg:#3A95C7)$git_status[\uE0B0](#3A95C7 bg:#40A9E0)$time[\uE0B0](#40A9E0 bg:none) $all$character """ | |
| add_newline = true | |
| [directory] | |
| style = "bg:#1C4961 fg:white" | |
| [git_branch] | |
| format = "[ $symbol$branch ]($style)" |
| # This Makefile builds a shared version of the library, | |
| # libbz2.dylib for MacOSX x86 (10.13.4 or higher), | |
| # with gcc-2.96 20000731 (Red Hat Linux 7.1 2.96-98). | |
| # It is a custom Makefile. Use at own risk. | |
| # Run in your MacOS terminal with the following command: | |
| # make -f Makefile-libbz2_dylib | |
| PKG_VERSION?=1.0.8 | |
| PREFIX?=/usr/local |
| library(recount) | |
| library(edgeR) | |
| #/ Get the counts from GTEx via recount as a SummarizedExperiment | |
| #/ => 1.3GB file | |
| options(timeout=600) | |
| download_study("SRP012682", type = "rse-gene") | |
| load(file.path("SRP012682", "rse_gene.Rdata")) | |
| #/ remove whitespaces in tissue names: |
| library(ggplot2) | |
| library(reshape2) | |
| library(egg) | |
| # thanks to https://stackoverflow.com/questions/1330989/rotating-and-spacing-axis-labels-in-ggplot2/60650595#60650595 | |
| dat<-reshape2::melt(data.frame(groupA=rnorm(20), | |
| groupB=rnorm(20), | |
| groupC=rnorm(20))) |
Through the GitHub API it is possible to retrieve individual files from a Git repository via, e.g. curl. To do so, first retrieve the content information for the relevant file (or folder):
curl https://api.github.com/repos/{organisation}/{repository}/contents/{file or folder path}
For private repositories, authenticate using your username and a personal access token
| #' --- | |
| #' output: | |
| #' md_document: | |
| #' pandoc_args: | |
| #' - '--from=markdown-implicit_figures' | |
| #' - '--to=commonmark' | |
| #' - '--wrap=preserve' | |
| #' --- | |
| # Stick this in your home directory and point your Global Git config at it by running: | |
| # | |
| # $ git config --global core.attributesfile ~/.gitattributes | |
| # | |
| # See https://tekin.co.uk/2020/10/better-git-diff-output-for-ruby-python-elixir-and-more for more details | |
| *.c diff=cpp | |
| *.h diff=cpp | |
| *.c++ diff=cpp | |
| *.h++ diff=cpp |