Inspired by article “How to set up and run Python Data Science Development Environment with Jupyter on Docker” [Archived] Data Scientists coders must work with a variety of Data Science development tools, including the Anaconda (or Miniconda) Python distribution platform, the Python programming language, the R programming language, Matplotlib library, Pandas Library, the Jupyter application, and many others. The article describes how to… Read More »
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 »
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 »
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 »
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 »
Re: omictools.com Finding software that is relevant to any biological analysis can be inspired by reading a paper or perhaps searching within Google. The web site https://omictools.com/ 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 »