Bioinformatics studies usually includes gene symbols as identifiers (IDs) as they are more recognizable comparing to other IDs such as Entrez IDs. However, certain analyses (tools) may not use gene symbols as there are usually more than one symbol so it is more difficult to implement a method to work with gene symbols. In such cases, you may need to do a conversion which is very common thing to do in bioinformatics.
You may have to keep both Python version, the old 2 and 3, at the same time due to your projects and they will require corresponding pip installation so you can separately install and maintain packages for both version.
Chrome’s new Developer Tools has a way to capture high quality full size screenshot of the page so you don’t have to have an extension for it anymore!
I had some issues installing Valgrind on macOS High Sierra and posted some tips to successfully install it to the system. Although I could install the software this way, it didn’t work correctly after testing with with several real and dummy C++ codes. It was giving me a memory leak error even with an empty code. So, then I decided to use an Ubuntu 16.04 based Docker container to test the code within the container using the Ubuntu version of Valgrind.
hg38/GRCh38 is the latest human reference genome as of today which was released December, 2013. There are multiple sources for downloading it and also it comes in different versions.
Valgrind is a programming tool for memory debugging, memory leak detection and profiling. Its installation for macOS High Sierra seems problematic and I wanted to write this post to tell the solution that worked for me. I use Homebrew to install it which is the recommended way and the solution also uses it.
Daha önceki bir yazımda Jupyter’in kurulumundan ve Jupyter Notebook‘tan bahsetmiştim. Jupyter’in kurulumu Jupyter Notebook’a Python kernelini direkt kuruyor ve Python ile programlamayı mümkün kılıyor ancak biyoenformatikte sıkça kullanılacak bir diğer programlama dili olan R programlama için ilgili kerneli ekstra kurmak gerekiyor. Bu yazımda bu kernelin kurulumundan bahsedeceğim.
Jupyter çeşitli programlama dilleri için etkileşimli bir ortam sağlayan yazılımdır. Orijinal olarak IPython (interactive python) adıyla, Python programlama dili için geliştirildi ancak daha sonra kurucuları Jupyter projesini başlatıp IPython’ın birçok tarafını Jupyter’e kaydırdı. IPython, sadece Jupyter’in kerneli olarak devam ediyor.
Recently, I have been trying to transfer my old posts in a Blogger blog to my new Jekyll blog since I really liked this way of blogging. But there were some features that I like in Blogger and wasn’t supported in Jekyll by default. I did some research and found a very nice way of generating tags cloud the my blog.
MySQL Workbench makes it really easy to generate EER diagrams from SQL scripts. Follow below steps to make one for yourself.