Passwordless SSH for Mac/Linux
You don’t have to enter the ssh password everytime you make a connection. Use below method to generate a key, copy it to the host you want to connect and connect anytime without entering your password.
Computing Significance of Overlap between Two Sets using Hypergeometric Test
There are many cases where we have two sets (e.g. under two different conditions) of things such as transcripts, genes or proteins and we want to compute the significance of the overlap between them. Hypergeometric test is very simple and widely used option for such cases.
ODTÜ Enformatik Enstitüsü'nün 20. Yılı Etkinliği
ODTÜ Enformatik Enstitüsü kuruluşunun 20. yılını bir bilim festivaliyle kutluyor. 16 Mayıs 2016‘da, ODTÜ Kültür ve Kongre Merkezi‘nde gerçekleştirilecek olan bilim festivaline herkes davetlidir!
Mann Whitney U Test (Wilcoxon Rank-Sum Test) Javascript Implementation
Currently Javascript is really poor in statistical methods compared to Python (SciPy) and R. There are several efforts to fill this gap, most notably from jStat. However, still many functions, distributions and tests are missing in this library. In one of my projects, I had to implement a Javascript version of Mann Whitney U test (or also called Wilcoxon rank-sum test). Here, I’m giving a link to its source code and describing how it works.
MiClip 1.3 Installation
MiClip is a CLIP-seq data peak calling algorithm implemented in R but currently it doesn’t show up in the CRAN but you can obtain it from the archive and install from the source or tar.gz file.
Generating 2D SVG Images of MOL Files using RDKit Transparent Background
The latest release of RDKit (2015-03) can generate SVG images with several lines of codes but by default the generated SVG image has a white background. The investigations on sources didn’t solve my problem as I couldn’t find any option for setting background to transparent background.
Install Cairo Graphics and PyCairo on Ubuntu 14.04 / Linux Mint 17
Cairo is a 2D graphics library implemented as a library written in the C programming language but if you’d like to use Python programming language, you should also install Python bindings for Cairo.
Install RDKit 2015-03 Build on Ubuntu 14.04 / Linux Mint 17
RDKit is an open source toolkit for cheminformatics. It has many functionalities to work with chemical files.
Generating 2D Images of Molecules from MOL Files using Open Babel
Open Babel is a tool to work with molecular data in any way from converting one type to another, analyzing, molecular modeling, etc. It also has a method to convert MOL files into SVG or PNG images to represent them as 2D images.
Simple Way of Python's subprocess.Popen with a Timeout Option
subprocess module in Python provides us a variety of methods to start a process from a Python script. We may use these methods to run an external commands / programs, collect their output and manage them. An example use of it might be as following: