Default preference reversal in R 4.0.x

I just wrote an entry on my Biochem blog which I think would fit on this site: Default preferences I enjoy using R and RStudio, but I am always weary of upgrading R because that usually leads to some issue(s). The most recent was a bit long for me to diagnose, even though in retrospect… Read More »

“bashing” PowerShell

Even though PowerShell has been around for apparently a long time (cerca 2002) it only came onto my “radar” recently as the “app” that can be used as a Text-Terminal to ssh somewhere. But I was then surprised to discover that in fact PowerShell also exists for MacOS as well as Linux! So I looked a… Read More »

in2csv: the Excel killer is part of csvkit the command-line spreadsheet

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: thomasleplus/csv Inspiration: stack overflow article: convert-xlsx-file-to-csv-using-batch Note: I wrote a different version of this on this post elsewhere: csvkit command-line spreadsheet can convert and… Read More »

A great Unix tutorial suitable for beginners

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 titled “Unix for Neuroimagers”  provides a wonderfully well done, easy to understand set of small… Read More »

PCA as Metro-Maps & Hierarchical Clustering on Principal Components

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 discussed in my previous post here (and there.) “Metro Maps” Today while revisiting the Wikipedia link for this dataset (Iris_flower_data_set) my… Read More »

TableConvert.com – free tabular data formats converter

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 Kaesberg to learn cloning and sequencing, I was surprised when he said that the most important program to work with sequences was the (now defunct GCG) program… Read More »

Bioawk for handling bioinformatics formats

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 GitHub: github.com/vsbuffalo/bioawk-tutorial I also found a recent docker image, and in fact there are only 2 images on docker hub: lbmc/bioawk updated 2 months ago,… Read More »

A Boy And His Atom: The World’s Smallest Movie

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 scanning probe microscopes revolutionized nanoscience” (link.) The article is progressing over time from 1993 til… Read More »

GREP was written overnight – Birth and Name

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 came  from. See video below, titled “Where GREP Came From – Computerphile” Summary: this comes from the command g/re/p… Read More »

Visualizing gzipped compressed text files

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” (“Future’sEnd” – StarTrek:Voyager, Season 3, episodes 50 & 51) and so my last post being… Read More »