My final submission for the Applied Data Science Capstone project from the IBM Data Science Professional certification offered by Coursera. All the code for this project can be found on the dedicated GitHub repository. Introduction In a few months, I’m moving to Cambridge, UK to start a new job as a…

Most commonly, data are shared and worked with using a tabular format, which means observations are stored in rows and variables in columns. Based on the number of available rows and columns, the file size of these data can range from a few KB to many GB. There is also…

XML is a markup language used to represent and distribute data structures which can be often difficult to create using more standard tabular formats. Basically, the XML format is similar to HTML (which is another markup language, indeed), in that data are organised in elements, which define the type of…

When you need to concatenate a Python string with some variables, there are actually several ways to achieve the same results. Some of them are quite basic, others are less recommended, but all of them are equally efficient for string formatting purposes. The basic way The simplest method for concatenating strings and variables…

The Linux PATH is an environmental variable that contains all the directories that the shell will search for executable files, when a user issues a command. It can be modified temporarily or permanently in order to include specific software, so that having to type the whole path of that software…

One of the most important things to do after setting up a new Linux server (or after taking over an existing one) is to create a new user, possibly with sudo powers. …

Next Generation Sequencing techniques have brought new insights into -omics data analysis, mostly thanks to their reliability in detecting biological variants. This reliability is usually measured using a value called Phred quality score (or Q score). The Phred score of a base is an integer value that represents the estimated…

A well-established bioinformatician usually has a handful of appropriate informatics tools to manipulate and analyse genomic data, for example counting sequences in a file. Nonetheless, in some cases it may be useful to rely on standard Unix commands, for example when your trusty laptop is not available or you’re working…

I often find myself looking for some shortcuts and quick commands while working in the Unix terminal, so here is a list of the most useful ones to perform common tasks. File system ls – list items in the current directory ls -l – list items in the current directory in a long…