kbroman

bsag

This is a silly little private layer I put together for Spacemacs to allow me to open the current (Markdown) buffer in Marked 2.app when I hit the key combo SPC om. Since I am very new to both Emacs and Spacemacs, I am not at all confident that the functions are in the appropriate places, and I am sure it could be done more simply. Having said all that, it works!

To activate it put the two .el files above within a folder called 'marked' within your 'private' folder (or whatever folder you have pointed dotspacemacs-configuration-layer-path at). Then you just need to add marked to your dotspacemacs-configuration-layers list in your .spacemacs.

ikirker

List of languages and whether there is a Bio- project

Language	Bio-
C	sort of
C++	Y
Python	Y
Ruby	Y
Java	Y
Perl	Y

dwinter

```{r, echo=FALSE}
knitr::opts_knit$set(upload.fun = knitr::imgur_upload, base.url = NULL)  
```


# and now, all animals and with nested taxonomic ranks

So, a few people liked [this example](https://gist.github.com/dwinter/8d7bde0579daf7466508) 
of using `rentrez` to investigate the taxonomic distribution of sequences in
Genbank. I though it might be fun to extend it a little. Specifically:

dwinter

#Finding the number of sequence records by taxonomic group

Ricardo wants to know how to find the number of sequence records associated with sub-groups within a given taxon . This example grew a bit too big to make into a comment, so here it is in gist form.

So, let's find out how many DNA sequences are present in genbank for each

isaacs

# Hello, and welcome to makefile basics.
#
# You will learn why `make` is so great, and why, despite its "weird" syntax,
# it is actually a highly expressive, efficient, and powerful way to build
# programs.
#
# Once you're done here, go to
# http://www.gnu.org/software/make/manual/make.html
# to learn SOOOO much more.

cboettig

#!/bin/bash

PORT=${PORT:=8787}

# Mac/Windows must get this from boot2docker
IP=${IP:="http://localhost"}

# Pull latest version?  (Allowed to fail, in case of no internet etc)
docker pull rocker/rstudio || true

kbroman

A regular code chunk:

```{r regular}
data(cars)
summary(cars)
```

A verbatim code chunk:

bsag

" Set up Vundle to manage plugins
set nocompatible
filetype off

" set the runtime path to include Vundle and initialize
set rtp+=~/.vim/bundle/vundle/
call vundle#rc()

" let Vundle manage Vundle, required
Plugin 'gmarik/vundle'

jwreagor

{
/* Keybindings for emacs emulation.  Compiled by Jacob Rus.
 *
 * This is a pretty good set, especially considering that many emacs bindings
 * such as C-o, C-a, C-e, C-k, C-y, C-v, C-f, C-b, C-p, C-n, C-t, and
 * perhaps a few more, are already built into the system.
 *
 * BEWARE:
 * This file uses the Option key as a meta key.  This has the side-effect
 * of overriding Mac OS keybindings for the option key, which generally