Statistical analysis made easy in Python | Randal S. Olson

http://www.randalolson.com/2012/08/06/statistical-analysis-made-easy-in-python/

PLINK 1.9 for genomic data analysis

https://www.cog-genomics.org/plink2/

Command line one-liners | Arturo Herrero

http://arturoherrero.com/2013/11/29/command-line-one-liners/

PLOS ONE: DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072614

healthvis | Interactive visualization in health: Package version 1.2

R with D3 graphics, check out their survival plot.

http://healthvis.wordpress.com/

The Art of Unix Programming

http://www.faqs.org/docs/artu/

Join command combines two data file on similar field

http://blog.comsysto.com/2013/04/25/data-analysis-with-the-unix-shell/

It is also possible to make joins in the Unix shell with the command called join. The join command assumes that input data is sorted based on the key on which the join is going to take place. You can find another dataset on github which contains countries. This dataset is a comma separated list as well. The 14th column in the country dataset represents the capital id which is similar to the id in the city data set. This makes it possible to create a list of countries with their capitals.

1 2 3 4 5 6 7 8 9

bz@cs ~/data/ $ cat city | head -n 2     1,Kabul,AFG,Kabol,1780000     2,Qandahar,AFG,Qandahar,237500 bz@cs ~/data/ $ cat country | head -n 2     AFG,Afghanistan,Asia,Southern and Central Asia,652090,1919,22720000,45.9,5976.00,,Afganistan/Afqanestan,Islamic Emirate,Mohammad Omar,1,AF     NLD,Netherlands,Europe,Western Europe,41526,1581,15864000,78.3,371362.00,360478.00,Nederland,Constitutional Monarchy,Beatrix,5,NL bz@cs ~/data/ $ join -t "," -1 1 -2 14 -o '1.2,2.2' city country | head -n 2     Kabul,Afghanistan     Amsterdam,Netherlands

Fwd: unix tips

Get some sampled data of a very big file

awk     'BEGIN { srand(systime()); } {if (rand() < 0.3) { print $0; } }'    data.csv

qstats – quick and dirty statistics tool for the Unix pipeline | On the lambda

http://www.onthelambda.com/2013/11/05/qstats-quick-and-dirty-statistics-tool-for-the-unix-pipeline/

# Print a multiplication table.

printf "%3d %3d %3d %3d %3d %3d %3d %3d %3d %3d\n" $( echo {1..10}*{1..10}\; | bc )

Linux Shell Scripting Tutorial | Learn Linux Shell Script - LinOxide

http://linoxide.com/category/linux-shell-script/

15 Linux Cat Command Examples For File Management - LinOxide

http://linoxide.com/linux-command/13-cat-command-examples/

Unbelievable ! 30 Linux TOP Command Examples With Screenshots - LinOxide

http://linoxide.com/linux-command/linux-top-command-examples-screenshots/

Famous Awk One-Liners Explained, Part I: File Spacing, Numbering and Calculations - good coders code, great reuse

http://www.catonmat.net/blog/awk-one-liners-explained-part-one/

My Job Interview at Google - good coders code, great reuse

http://www.catonmat.net/blog/my-job-interview-at-google/

Bash One-Liners Explained, Part II: Working with strings - good coders code, great reuse

New things.

http://www.catonmat.net/blog/bash-one-liners-explained-part-two/

Bash One-Liners Explained, Part I: Working with files - good coders code, great reuse

Unique content.

http://www.catonmat.net/blog/bash-one-liners-explained-part-one/

Which files/dirs waste my disk space | commandlinefu.com

http://www.commandlinefu.com/commands/view/12948/which-filesdirs-waste-my-disk-space

fish unix shell

Use it.

http://fishshell.com/

OpenRefine working with messy data

http://openrefine.org/

Tabula

http://tabula.nerdpower.org/

Extract tables from PDF FILES.

Linux tips | cut complement

cut -d: -f2-4,7 --complement </etc/passwd # Cut the complement of columns 2-4,7. So in other words, gives you 1,5-6,8-

Welcome to Bokeh — Bokeh 0.2 documentation

http://bokeh.pydata.org/

Seaborn: statistical data visualization — seaborn 0.2.dev documentation

http://stanford.edu/~mwaskom/software/seaborn/

Time-Saving Tricks on the Command Line | Linux Journal

http://m.linuxjournal.com/content/time-saving-tricks-command-line

Set Operations in the Unix Shell - good coders code, great reuse

http://www.catonmat.net/blog/set-operations-in-unix-shell/

Turn everything that is not a sequence of numbers, into a comma.

echo abc1defg23hi456 | sed -r 's/[^0-9]+/,/g' #

7 Handy Command Line Tips You Don’t Want to Miss

http://osxdaily.com/2013/10/17/7-handy-command-line-tips/

GNU Parallel - parallelize serial command line programs without changing them - BioStar

http://www.biostars.org/p/63816/#83597?utm_source=twitterfeed&utm_medium=twitter

Gnu parallel with bedtools jaccard

Pairwise Jaccard statistic on many files using GNU parallel:
parallel "bedtools jaccard -a {1} -b {2} ::: `ls f*bed` ::: `ls f*bed`

Split large file - Biopython

http://biopython.org/wiki/Split_large_file

Embedded Terminal - A Gedit Plugin To Access The Command Line Terminal From Within The Editor Window | MyLinuxBook

http://mylinuxbook.com/embedded-terminal-a-gedit-plugin/

Join Data Files on the Command Line

Your favorite join command

http://craig-russell.co.uk/2012/07/13/join-data-files-command.html#.UlLw_pC6aax

describe Function · GitHub

https://github.com/drbunsen/describe

7 command-line tools for data science

http://jeroenjanssens.com/2013/09/19/seven-command-line-tools-for-data-science.html

Shell command to sum integers, one per line? - Stack Overflow

http://stackoverflow.com/questions/450799/shell-command-to-sum-integers-one-per-line

# Order lines of a file by the length of the line descending.

awk '{print length($0),$0}' names.txt | sort -nr | cut -d' ' -f2-

Alternatives to a 3D Bar Chart - Peltier Tech Blog

http://peltiertech.com/WordPress/3d-bar-chart-alternatives/

Working with Structured Data Using Command Line Tools in Linux | William J Turkel

http://williamjturkel.net/2013/09/03/working-with-structured-data-using-command-line-tools-in-linux/

Linux Command Line Cheat Sheet by DaveChild - Cheatography.com

http://www.cheatography.com/davechild/cheat-sheets/linux-command-line/

Copy to drive. Genome Spot: A selection of useful bash one-liners

http://genomespot.blogspot.in/2013/08/a-selection-of-useful-bash-one-liners.html?utm_source=buffer&utm_campaign=Buffer&utm_content=buffer77494&utm_medium=twitter

Sort the output of df while keeping the header at the top.

df -hP | awk 'NR==1;NR>1{print|"sort -k5rn"}' #

Tweet from Unix tool tip (@UnixToolTip)

Unix tool tip (@UnixToolTip) tweeted at 6:33 PM on Sat, Aug 24, 2013:
Form complementary DNA: sed s/ATCG/TAGC/g
(https://twitter.com/UnixToolTip/status/371256361197514752)

Get the official Twitter app at https://twitter.com/download

pipes.sh: Animated pipes terminal screensaver.

https://gist.github.com/livibetter/4689307

Using Names Pipes and Process Substitution in Bioinformatics

http://vincebuffalo.org/2013/08/08/the-mighty-named-pipe.html

Give me that one command you wish you knew years ago. I'll start. : linux

http://www.reddit.com/r/linux/comments/mi80x/give_me_that_one_command_you_wish_you_knew_years/

The Linux Command Line by William E. Shotts, Jr.

http://linuxcommand.org/tlcl.php

ssh aliases | alias.sh

http://alias.sh/category/46

Bash One-Liners :: bashoneliners.com

http://www.bashoneliners.com/oneliners/oneliner/

bash - Associative arrays in Shell scripts - Stack Overflow

http://stackoverflow.com/questions/688849/associative-arrays-in-shell-scripts?rq=1

UNIX and Linux Shell Variables

http://www.itforeveryone.co.uk/shellSpecialVariables.html

Learning the UNIX command line

http://us7.campaign-archive1.com/?u=fd1f24aadaae48b22d7d03a3b&id=781a06d7a7

Quickly navigate your filesystem from the command-line

http://jeroenjanssens.com/2013/08/16/quickly-navigate-your-filesystem-from-the-command-line.html