Jean-Yves Sgro

Summary

csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. (csvkit can convert XLSX files to CSV.)
A good docker container for csvkit: […]

More than once I have written my own tutorials for learning how to use the command line within the bash shell in the context of a Unix or Unix-like computer. Recently I found a very well done tutorial that, while […]

The iris dataset is perhaps one of the most famous datasets used to learn and teach statistics and now machine learning. Being curious about this dataset lead me last time to the TableConvert.com  web site that I […]

This is a repost of my post on the Biochemistry department: tableconvert-com-free-tabular-data-formats-converter
Tabular formats
When I first came to Madison in 1986 as a postdoc with Biochemistry professor Paul […]

Today I found a new tool: bioawk that was written by Heng Li who also wrote samtools and bwa.

I first discovered it ont this blog: bioawk-basics (Bioinformatics Workbooks)

There is also a short tutorial on GitH […]

Moving atoms
For some reason a paper copy of “Chemical and Engineering News” (November 11, 2019 – Vol 97 Issue 44) ended up in my hands, and I almost missed this fun section named: “30 years of moving atoms: How […]

I use grep very often, and I made-up and acronym that made sense to me: Get REgular ExPression

But I discovered this YouTube video that gives an accurate historical recounting of its birth and where its name […]

Even though I have been using computers all my life there are still many aspects of computing that are mysterious to me, and I am sure many others…

One of my favorite quotes is “A leads to B leads to C” […]

Binder 2.0
As just an “end-user” of software for data analysis it is sometimes difficult to just catch up with what’s available, and I end-up discovering new things simply browsing the web looking for something […]

Recently I was testing a Docker image to run a container for Next Gen sequencing, a way to test an existing “pipeline” on the first published study of the effect of the Zika virus. […]

Downsampling
I have performed a search for creating a set of down-sampled data from an actual  large dataset, and while there are many creative information on BioStar and other forums, I find that the most […]

I have started a series of tutorials that I am writing from the perspective of a biologist wanting to use a Docker container for a specific application.

An easy example could be using EMBOSS, the molecular […]

Re:  pythonhosted.org/omics_pipe

Next Gen. data analysis requires many steps, that can be learned one by one, for example running an aligner such as bowtie, tophat or STAR, then handle the SAM/BAM file for […]

Re:alternativeto.net

What software one uses may be the result of colleague recommendations, using “what others use in the lab,” or haphazardly found options online.

Or perhaps it is time to “upgrade” a […]