antonkratz

#!/usr/bin/Rscript

# author: Anton Kratz
# created: Fri Jul 20 11:00:06 PDT 2018

# given a graph in edge list with score field, i.e.:
# FROM_NODE TO_NODE SCORE
# determine the # of components in this graph

suppressPackageStartupMessages(library(igraph))

antonkratz

# Anton Kratz
# date: Sat Jul 21 17:03:22 PDT 2018
suppressPackageStartupMessages(library("igraph"))
suppressPackageStartupMessages(library("ggplot2"))

# Load the PG Yeast Net file - two large components and many small ones 
rf <- read.table("~/git/assets/INT.PG.YeastNet.v3.2463gene.54496link.txt", sep="\t")
akg <- graph_from_data_frame(rf, directed = FALSE, vertices = NULL)

# List of degrees

antonkratz

find . -type f -exec \
bash -c 'md5sum "$0" | grep -q b2a490745fe5fe8a41c0d1040faff507 && echo $0' {} \;

https://superuser.com/questions/653185/finding-a-file-by-md5sum

antonkratz

find ./ | sed -e 's/[^-][^\/]*\//--/g;s/--/ |-/'

antonkratz

Building a separate database enables you to locate files on sshfs-mounted filesystems

The find command is very slow. locate is much faster, but relies on a database, which is typically build nightly. Often I have mounted remote filesystems using sshfs. By default, the database is not build for sshfs-mounted filesystems.

Build an mlocate database for the sshfs-mounted dir /home/kratz/mpoints/cellar (see below for cron version):

updatedb -l 0 -o ~/.cellar.db -U /home/kratz/mpoints/cellar

antonkratz

Disable the caps lock key entirely

Ubuntu

setxkbmap -option "caps:none"

antonkratz

You might run into a situation where git log, man man display absolutely nothing. This could be b/c bash forgot the PAGER variable. How this is possible is beyond me. You must reset the PAGER variable and then it will work again:

export PAGER=less

antonkratz

# author:   Anton Kratz
# created:  Mon Dec 17 19:08:48 PST 2018

# Based on original code by Mike Yu which is at [1]. However [1] has various NDEX and other
# code intermingled which is not necessary in this context. Also, I am building a similarity
# table for DNA repair on the fly.

# [1] https://github.com/michaelkyu/ddot/blob/master/examples/Process_the_Gene_Ontology.ipynb

import requests

antonkratz

Installing R on your own machine

The main guide on how to install R for any flavour of linux, binary or from source, is at http://cran.stat.ucla.edu/

Three different pathways to a working install, from simple to hard:

• use the distributions package manager (easiest but not the most recent version)
• install binary (recommended)
• compile and install from source

I am assuming you are on Ubuntu 16.04 LTS.

antonkratz

Cytoscape 3.7.1

the layout is too dense and I want to expand the layout

Layout --> Node layout Tools --> Scale:

when I zoom out, the text on the label dissappears