stevekm

Get OS Updates

sudo apt-get update && sudo apt-get dist-upgrade

install R https://www.r-bloggers.com/how-to-install-r-on-linux-ubuntu-16-04-xenial-xerus/

1. Add R repository

stevekm

Set up a new git repository (if it doesn't already exist, otherwise skip this step)

$ cd git_test/

$ ll
total 36K
drwxr-s--- 2 kellys04 kellys04   0 Sep 21 13:43 .
drwxr-s--- 4 kellys04 kellys04 350 Sep 21 13:43 ..

stevekm

Plot.ly Volcano Plot Example

Stephen Kelly
9/24/2016

# install.packages("plotly")
# install.packages("ggplot2")

stevekm

#!/usr/bin/env python
# python 2.7

# various ways to try to find and return the files in a given directory
# some of these are ok, some are bad, some are real real bad

import os
import re
import glob

stevekm

Plot.ly Volcano Plot Example

Stephen Kelly
9/24/2016

In this example, I will demonstrate how to use gene differential binding data to create a volcano plot using R and Plot.ly. This dataset was generated by DiffBind during the analysis of a ChIP-Seq experiment. Each entry represents a bound peak that was differentially expressed between groups of samples.

First, install any libraries you might not have, load the Plot.ly library, and load the file containing your differential binding data.

stevekm

Setup for GitHub Pages on MacBook with OS X El Capitan https://help.github.com/articles/setting-up-your-github-pages-site-locally-with-jekyll/

Forget the other junk, use this guid:

http://railsapps.github.io/installrubyonrails-mac.html

works perfectly!

https://help.github.com/articles/creating-pages-with-the-automatic-generator/

stevekm

I think this is where I was trying to get Docker installed

[2016-10-06 09:14:50]
steve@quark2:~$ grep -i 'docker' ~/.bash_history 
cat /etc/apt/sources.list.d/docker.list
touch /etc/apt/sources.list.d/docker.list
sudo touch /etc/apt/sources.list.d/docker.list
nano /etc/apt/sources.list.d/docker.list
sudo nano /etc/apt/sources.list.d/docker.list

stevekm

$ cat data/depth13Genome.depth.summary2.averages_sd.txt | cut -f1
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16

stevekm

http://stackoverflow.com/questions/6190331/can-i-do-an-ordered-default-dict-in-python

# from collections import OrderedDict, defaultdict
import collections
class OrderedDefaultDict(collections.OrderedDict, collections.defaultdict):
    def __init__(self, default_factory=None, *args, **kwargs):
        #in python3 you can omit the args to super
        super(OrderedDefaultDict, self).__init__(*args, **kwargs)
 self.default_factory = default_factory

stevekm

• Convert multipage PDF into single page PNG files with GhostScript

http://superuser.com/questions/350201/convert-many-images-to-one-pdf-on-mac/854606?noredirect=1#comment1639104_854606

gs -o /path/to/output_page_%03d.png -sDEVICE=png16m -r150 /path/to/input.pdf

• Convert multiple single-page PDF files into one multi-page PDF file