joyrexus

collapsible markdown?

CLICK ME

yes, even hidden code blocks!

print("hello world!")

Lenbok

#PED format pedigree
#
#fam-id/ind-id/pat-id/mat-id: 0=unknown
#sex: 1=male; 2=female; 0=unknown
#phenotype: -9=missing, 0=missing; 1=unaffected; 2=affected
#
#fam-id ind-id  pat-id  mat-id  sex     phen
1       NA12878 NA12891 NA12892 2       0 
1       NA12891 0       0       1       0
1       NA12892 0       0       2       0

jtleek

library(png)
library(ggforce)
library(animation)
library(tweenr)

jhu_png = readPNG("jhudsl.png")
x = rep(1:510,each=555)
y = rep(1:555,510)
val = jhu_png[,,3]
val = round(val)

davedelong

#!/bin/bash

# A script to automatically switch to another user in macOS
# Invoke like this: `autologin.sh {user} {password}`

uid=`id -u $1`

/System/Library/CoreServices/Menu\ Extras/User.menu/Contents/Resources/CGSession -switchToUserID "$uid"

osascript <<EOD

hadley

If you were to give recommendations to your "little brother/sister" on things that they need to do to become a data scientist, what would those things be?

I think the "Data Science Venn Diagram" (http://drewconway.com/zia/2013/3/26/the-data-science-venn-diagram) is a great place to start. You need three things to be a good data scientist:

• Statistical knowledge
• Programming/hacking skills
• Domain expertise

Statistical knowledge

arq5x

# assumes that the BEDGRAPH is the output of the bedtools genomecov tool using the -bga option.
$ cat foo.bedg
chr1	0	10	5
chr1	10	20	5
chr1	20	30	10
chr1	30	40	11
chr1	40	50	9
chr1	50	60	10
chr1	60	70	11
chr1	70	80	15

shrayasr

# Create a directory
mkdir ~/tmux-install
cd ~/tmux-install

# Get the files
curl -OL http://downloads.sourceforge.net/tmux/tmux-1.5.tar.gz
curl -OL http://downloads.sourceforge.net/project/levent/libevent/libevent-2.0/libevent-2.0.16-stable.tar.gz

# Extract them 
tar xzf tmux-1.5.tar.gz

rgbkrk

#!/usr/bin/env bash

# HubCrypt
# ========
#
# Decrypt a file encrypted using hubencrypt (ok, it's just openssl + rsautl +
# your SSH keys). It needs the private key that matches your last public key
# listed at github.com/<user>.keys
#

nathanhaigh

#!/bin/bash
# Usage: interleave_fastq.sh f.fastq r.fastq > interleaved.fastq
# 
# Interleaves the reads of two FASTQ files specified on the
# command line and outputs a single FASTQ file of STDOUT.
# 
# Can interleave 100 million paired reads (200 million total
# reads; a 2 x 22Gbyte files), in memory (/dev/shm), in 6m54s (414s)
# 
# Latest code: https://gist.github.com/4544979

nathanhaigh

#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
# 
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
# 
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
#