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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 specific, and ending up finding something else… that was the case for Docker a couple years ago. Today (Dec 30,2019)… Read More »
SRA: Sequence Read Archive The Sequence Read Archive (SRA) makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms, […] However, it is rather difficult to even find the download links… and even… Read More »
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 biology open suite for analysis. The tutorials are online at the Biochemistry department here: Docker tutorials (general page) Docker… Read More »