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bioinformatics

TableConvert.com – free tabular data formats converter

Posted on January 28, 2020

Tabular formats When I first came to Madison in 1986 as a postdoc with Biochemistry professor Paul Kaesberg to learn cloning and sequencing, I was surprised when he said that the most important program to …

Posted in bioinformatics, Programming, R

Dockerization – details needed

Posted on December 16, 2019

Reproducible research Docker is a great tool to provide methods for reproducible research that should allow other researchers to reproduce any advanced calculations that you, as a researcher have done, most likely in association with …

Posted in bioinformatics, Docker, Programming, Python

Finding alternate software

Posted on December 10, 2019

A couple years ago I wrote a short note on another blog (DNA.today – link below) about a web site that can be quite useful: it provides the name of alternate software. The site is: alternativeto.net For example, …

Posted in bash, bioinformatics, Molecular Graphics, Programming, Statistics

Survival command line

Posted on December 3, 2019

The built-in Terminal in MacOS and Linux and in Windows with added software provides access to the core of the computer. They are simply a software version (an emulation) of what used to be a hardware …

Posted in bash, bioinformatics, Docker, Programming

Docker saves the day – Roadmaps – rivem

Posted on November 26, 2019

Docker saves the day! Here is a great example of how Docker can help save a NATURE paper! Summary: Problem: Professor wants to use a specific virology program called rivem (links below.) However, this only works …

Posted in bioinformatics, Docker, Virology

How to spot a misleading graph?

Posted on November 22, 2019

As biochemists and biologists, like all scientists we convey results in the form of graphs. We also read papers that present results. More generally graphs are used in many aspects of every day news… The …

Posted in bioinformatics, Programming, StatisticsTagged analysis, bias, graphs, plots, results, statistics

Bioinformatics – which computer language should I learn first?

Posted on November 21, 2019

In the past years I have focused on what seemed to be the most useful bioinformatics tools for biologists that need to analyze data with software that does not have a graphical interface. The final …

Posted in bash, bioinformatics, Programming, Python, RTagged bioinformatics, computer language, data analysis, programming, python, R, RStudio
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