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).

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# 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, 

stephenturner

#!/bin/bash

# Uses the http://textbelt.com/ API to send a text message.
# The PHONE environment variable must be set, e.g., in your .bashrc., e.g.
# export PHONE=1234567890

# Usage: txt "<a text message to send>"

# Example 1
# When long_running_command is done successfully, this command

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stephenturner

library(rvest)
library(dplyr)
library(readr)

# How many pages do you want to harvest (currently over 10,000 available)
npages <- 5
for (i in 1:npages) {
  # If first time through the loop, initialize list to hold results
  if (i==1) d <- list()
  # Report progress

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> library(dplyr)
> 
> d1 <- data_frame(gene=c("g1", "g2", "g3"), expr=c(10, 20, 30))
> d1
Source: local data frame [3 x 2]

   gene  expr
  (chr) (dbl)
1    g1    10
2    g2    20

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# Function to merge topTable output with original expression values
mergett <- function(tt, eset) {
    if (class(tt)!="data.frame") stop("tt should be a data.frame")
    if (class(eset)!="ExpressionSet") stop("eset should be an ExpressionSet")
    exprset <- data.frame(exprs(eset))
    exprset$ID <- rownames(exprset)
    rownames(exprset) <- NULL
    print(paste("nrow(tt):", nrow(tt)))
    print(paste("nrow(exprset):", nrow(exprset)))
    if (nrow(tt)==nrow(exprset)) {

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library(dplyr)
library(AnnotationDbi)
library(org.Mm.eg.db)
ls("package:org.Mm.eg.db")

entrez2alias <- org.Mm.egALIAS2EG %>%
  as.list %>%
  unlist %>%
  data_frame(entrez=., alias=names(.))
head(entrez2alias)

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