mikelove

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

JosiahParry

# 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

strengejacke

// 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))

notheotherben

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)"

obihill

# 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

ATpoint

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:

ATpoint

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)))

fkraeutli

How to retrieve GIT LFS files from GitHub

Retrieving non-LFS files

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

kelly-sovacool

#' ---
#' output:
#'   md_document:
#'     pandoc_args:
#'       - '--from=markdown-implicit_figures'
#'       - '--to=commonmark'
#'       - '--wrap=preserve'
#' ---

tekin

# 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