yihui

See http://animation.r-forge.r-project.org/knitr/ for a preview of all knitr themes in HTML, and http://rclickhandbuch.files.wordpress.com/2014/09/knitrthemesoverview.pdf for a preview in LaTeX (credit to Berry Boessenkool).

The knitr themes manual can be found at (Rnw source).

hinkelman

n = 100                             # No. of samples per treatment
mean.A = 10                         # Mean count for treatment A
mean.B = 5                          # Mean count for treatment B
nd = data.frame(Trt = c("A", "B"))  # Used in predict( ) function

# Generate example data based on Poisson distribution (mean = variance)
data.pois = data.frame(Trt = c(rep("A", n), rep("B", n)), 
                       Response = c(rpois(n, mean.A), rpois(n, mean.B))
                       )

swarminglogic

#!/bin/bash

# $1: PID
# Returns true if a process exists with pid=PID
function isProcessAlive  {
    if [ `ps -p $1 | wc -l` -gt 1 ] ; then
        return 0;
    else
        return 1;
    fi

jbryer

#' Simplified loading and installing of packages
#'
#' This is a wrapper to \code{\link{require}} and \code{\link{install.packages}}.
#' Specifically, this will first try to load the package(s) and if not found
#' it will install then load the packages. Additionally, if the 
#' \code{update=TRUE} parameter is specified it will check the currently 
#' installed package version with what is available on CRAN (or mirror) and 
#' install the newer version.
#' 
#' @param pkgs a character vector with the names of the packages to load.

stephenturner

## RNA-seq analysis with DESeq2
## Stephen Turner, @genetics_blog

# RNA-seq data from GSE52202
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

# Import & pre-process ----------------------------------------------------

# Import data from featureCounts

alimuldal

import numpy as np
from scipy import stats
from itertools import combinations
from statsmodels.stats.multitest import multipletests
from statsmodels.stats.libqsturng import psturng
import warnings


def kw_dunn(groups, to_compare=None, alpha=0.05, method='bonf'):
    """

jslefche

Black theme for ggplot2

This is an additional theme for ggplot2 that generates an inverse black and white color scheme.

Example

ggplot(mtcars, aes(wt, mpg)) + geom_point()
# Add theme_black()
ggplot(mtcars, aes(wt, mpg)) + geom_point(color = "white") + theme_black()

paulirish

Option 1: Command-line download extension as zip and extract

extension_id=jifpbeccnghkjeaalbbjmodiffmgedin   # change this ID
curl -L -o "$extension_id.zip" "https://clients2.google.com/service/update2/crx?response=redirect&os=mac&arch=x86-64&nacl_arch=x86-64&prod=chromecrx&prodchannel=stable&prodversion=44.0.2403.130&x=id%3D$extension_id%26uc" 
unzip -d "$extension_id-source" "$extension_id.zip"

Thx to crxviewer for the magic download URL.

Changaco

#!/bin/bash
# btrfs-undelete
# Copyright (C) 2013 Jörg Walter <info@syntax-k.de>
# This program is free software; you can redistribute it and/or modify it under
# the term of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or any later version.

if [ ! -b "$1" -o -z "$2" -o -z "$3" ]; then
	echo "Usage: $0 <dev> <file/dir> <dest>" 1>&2
	echo

RichardBronosky

#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""This module's docstring summary line.

This is a multi-line docstring. Paragraphs are separated with blank lines.
Lines conform to 79-column limit.

Module and packages names should be short, lower_case_with_underscores.
Notice that this in not PEP8-cheatsheet.py