Category Archives: Computation

“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  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 »

Beyond Docker? Binder 2.0

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 »

Review on Deep Learning in Biology and Medicine

Deep neural networks are everywhere. They are revolutionizing our day-to-day lives, and this phenomenon no longer needs any introduction or description. Deep learning is especially suitable to find structures in overwhelming amounts of data. Recently, biological data became exactly that – overwhelming, and application of deep learning toolsets to it indeed looks very natural. You… Read More » finding alternate software 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 commercial package and the steep price makes you think twice… The crowdsources software recommendation web site does just that… just enter the name… Read More » Search engine for biological data analysis

Re: Finding software that is relevant to any biological analysis can be inspired by reading a paper or perhaps searching within Google. The web site contains 16,971 software (omic) tools that are organized in categories shown on the home page. Checking a bit further one can find interesting entries such as: High-throughput sequencing data analysis…… Read More »