stephenturner

#!/usr/bin/python

import sys

header=True
for line in sys.stdin:
    if line.startswith('##'):
        if header:
            print line.strip()
        continue

stephenturner

// Place your key bindings in this file to overwrite the defaults
[
    // RStudio: Copy lines up/down with alt+cmd+up/down
    {
        "key": "alt+cmd+down",
        "command": "editor.action.copyLinesDownAction",
        "when": "editorTextFocus && !editorReadonly"
    },
    {
        "key": "shift+alt+down",

stephenturner

[
    // Auto-pair backticks
  { "keys": ["`"], "command": "insert_snippet", "args": {"contents": "`$0`"}, "context":
    [
      { "key": "setting.auto_match_enabled", "operator": "equal", "operand": true },
      { "key": "selection_empty", "operator": "equal", "operand": true, "match_all": true },
      { "key": "following_text", "operator": "regex_contains", "operand": "^(?:\t| |\\)|]|\\}|>|$)", "match_all": true },
      { "key": "preceding_text", "operator": "not_regex_contains", "operand": "[`a-zA-Z0-9_]$", "match_all": true },
      { "key": "eol_selector", "operator": "not_equal", "operand": "string.quoted.single", "match_all": true }
    ]

stephenturner

<script language="JavaScript">
$(function() {
  /* Lets the user click on the images to view them in full resolution. */
  $("div.figure img").wrap(function() {
    var link = $('<a/>');
    link.attr('href', $(this).attr('src'));
    link.attr('title', $(this).attr('alt'));
    link.attr('target', '_blank');
    return link;
  });

stephenturner

## devtools::install_github("stephenturner/msigdf")
library(msigdf)
library(dplyr)
library(clusterProfiler)

c2 <- msigdf.human %>% 
    filter(collection == "c2") %>% select(geneset, entrez) %>% as.data.frame

data(geneList)
de <- names(geneList)[1:100]

stephenturner

# Performs principal components analysis on an ExpressionSet
eset_pca <- function (eset) {
  mypca <- prcomp(t(na.omit(exprs(eset))))
  pca <- as.data.frame(mypca$x)
  pc1var <- round(summary(mypca)$importance[2,1]*100, digits<-1)
  pc2var <- round(summary(mypca)$importance[2,2]*100, digits<-1)
  pc1lab <- paste0("PC1 (",as.character(pc1var),"%)")
  pc2lab <- paste0("PC1 (",as.character(pc2var),"%)")
  out <- merge(pData(eset), pca, by<-"row.names") %>% 
    dplyr::rename(id<-Row.names)

stephenturner

#!/bin/bash

# Nullarbor+dependencies installation script for a fresh Ubuntu 14.04 instance.


################################################################################
## Conveniences
################################################################################

# Some essential aliases

stephenturner

#!/usr/bin/env bash

# Configuration
remote_target=master
destination=_site

get-working-branch() {
    git status | head -n 1 | awk '{ print $NF }'
}

stephenturner

Deploying a subfolder to GitHub Pages

Sometimes you want to have a subdirectory on the master branch be the root directory of a repository’s gh-pages branch. This is useful for things like sites developed with Yeoman, or if you have a Jekyll site contained in the master branch alongside the rest of your code.

For the sake of this example, let’s pretend the subfolder containing your site is named dist.

Step 1

Remove the dist directory from the project’s .gitignore file (it’s ignored by default by Yeoman).

stephenturner

# The hook

```{r}
library(knitr)
knitr::knit_hooks$set(source = function(x, options){
  if (!is.null(options$verbatim) && options$verbatim){
    opts = gsub(",\\s*verbatim\\s*=\\s*TRUE\\s*", "", options$params.src)
    bef = sprintf('\n\n    ```{r %s}\n', opts, "\n")
    stringr::str_c(
      bef,