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Jean-Yves Sgro wrote a new post, Download Google Drive Files using wget 2 months, 1 week ago
Cross-posting from post: Download Google Drive Files using wget
The problem: transfer file between clouds
Files on Google drive can be shared between users, but the default access to the file is via we we […] -
Jean-Yves Sgro wrote a new post, macOS Catalina – when “Allow” does not appear in System Preferences 3 months, 2 weeks ago
The saying goes “if it ain’t broke don’t fix it!” – Oh Yeah. But sometimes it is inevitable…
Problem
Last month, under macOS Mojave (10.14) suddenly VMWare did not want to start, because of a security issue […] -
Jean-Yves Sgro wrote a new post, Default preference reversal in R 4.0.x 5 months, 2 weeks ago
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). […] -
Jean-Yves Sgro wrote a new post, “bashing” PowerShell 5 months, 4 weeks ago
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 […]
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Jean-Yves Sgro wrote a new post, in2csv: the Excel killer is part of csvkit the command-line spreadsheet 6 months, 2 weeks ago
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: […] -
Jean-Yves Sgro wrote a new post, A great Unix tutorial suitable for beginners 11 months, 2 weeks ago
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 […]
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Jean-Yves Sgro wrote a new post, PCA as Metro-Maps & Hierarchical Clustering on Principal Components 1 year, 2 months ago
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 […]
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Jean-Yves Sgro wrote a new post, TableConvert.com – free tabular data formats converter 1 year, 2 months ago
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 […] -
Jean-Yves Sgro wrote a new post, Bioawk for handling bioinformatics formats 1 year, 2 months ago
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 G […]
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Jean-Yves Sgro wrote a new post, A Boy And His Atom: The World’s Smallest Movie 1 year, 3 months ago
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 […] -
Jean-Yves Sgro wrote a new post, GREP was written overnight – Birth and Name 1 year, 3 months ago
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 […]
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Jean-Yves Sgro wrote a new post, Visualizing gzipped compressed text files 1 year, 3 months ago
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” […]
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Jean-Yves Sgro wrote a new post, Beyond Docker? Binder 2.0 1 year, 3 months ago
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 […] -
Jean-Yves Sgro wrote a new post, STAR index for human genome – overcoming the hardware barriers 1 year, 3 months ago
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. […]
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Jean-Yves Sgro wrote a new post, Down-sampling FASTQ.gz paired ends 1 year, 4 months ago
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 […] -
Jean-Yves Sgro wrote a new post, Hunting for SRA sequence archives 1 year, 4 months ago
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 S […] -
Jean-Yves Sgro wrote a new post, Docker tutorials for Biologists 1 year, 4 months ago
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 […]
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Yury Bukhman uploaded the file: PAG XXVI notes to
BioComP 3 years, 1 month ago
I have presented these notes at the BioComP meeting on 22 Jan 2018. They have been modified, mostly by rearranging the slides and adding hyperlinks to papers and software.
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Oleg Moskvin wrote a new post, Enterotypes-2018 3 years, 2 months ago
The recent update on enterotypes1 was an important read.
Yes, we desperately need to reduce the dimensionality of the gut microbiome data and discover the stable “archetypes” of the microbiome functional […]
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Oleg Moskvin started the topic Meeting notes – 23 Oct 2017 in the forum
BioComP 3 years, 5 months ago
This was the first meeting of the BioComP group in the new location – WID.
Presentation slides – “Deep Learning for Biological Data Analysis”
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