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<!DOCTYPE html>
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<title>Jeff Grover. Bioinformatics Scientist.</title>
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<h1><a href="https://groverj3.github.io">Jeffrey Grover</a></h1>
<p>Senior Scientist - NGS & Bioinformatics @ <a href="https://www.entradatx.com/" target="_blank">Entrada Therapeutics</a></p>
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<article>
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<h2><a href="https://groverj3.github.io/articles/2019-07-17_efficiently-filtering-while-reading-data-into-r-with-python.html#efficiently-filtering-while-reading-data-into-r-with-python">Efficiently Filtering While Reading Data Into R (With Python?!)</a></h2>
<p>
Posted on Wed 17 July 2019 in <a href="https://groverj3.github.io/category/how-to.html">how-to</a>
• Tagged with
<a href="https://groverj3.github.io/tag/bioinformatics.html">bioinformatics</a>, <a href="https://groverj3.github.io/tag/data-science.html">data-science</a>, <a href="https://groverj3.github.io/tag/r.html">r</a>, <a href="https://groverj3.github.io/tag/python.html">python</a>, <a href="https://groverj3.github.io/tag/big-data.html">big-data</a>
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<p>Working with large amounts of tabular data is a daily occurance for both
bioinformaticians and data scientists. There's a lot the two groups can learn
from each other (great future post material). However, I recently ran into a
situation that I was sure had to be relatively common. Apparently it …</p>
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<a class="btn" href="https://groverj3.github.io/articles/2019-07-17_efficiently-filtering-while-reading-data-into-r-with-python.html#efficiently-filtering-while-reading-data-into-r-with-python"> Continue reading
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<h2><a href="https://groverj3.github.io/articles/2019-07-09_variations-on-rnaseq-workflows-for-deg-analysis.html#variations-on-rnaseq-workflows-for-deg-analysis">Variations on RNAseq Workflows for DEG Analysis</a></h2>
<p>
Posted on Tue 09 July 2019 in <a href="https://groverj3.github.io/category/commentary.html">commentary</a>
• Tagged with
<a href="https://groverj3.github.io/tag/bioinformatics.html">bioinformatics</a>, <a href="https://groverj3.github.io/tag/thoughts.html">thoughts</a>, <a href="https://groverj3.github.io/tag/rnaseq.html">rnaseq</a>, <a href="https://groverj3.github.io/tag/workflows.html">workflows</a>
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<p>When analyzing RNAseq you're faced with many possible analysis pipelines. The
biggest decision you need to make is what the purpose of your experiment is. I
will make the assumption that <em>most</em> of the time people want to determine which
genes are differentially expressed between two samples, genotypes, conditions,
etc …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2019-07-09_variations-on-rnaseq-workflows-for-deg-analysis.html#variations-on-rnaseq-workflows-for-deg-analysis"> Continue reading
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<h2><a href="https://groverj3.github.io/articles/2019-06-28_making-better-metaplots-with-ggplot-part-2.html#making-better-metaplots-with-ggplot-part-2">Making Better Metaplots With ggplot, Part 2</a></h2>
<p>
Posted on Fri 28 June 2019 in <a href="https://groverj3.github.io/category/how-to.html">how-to</a>
• Tagged with
<a href="https://groverj3.github.io/tag/bioinformatics.html">bioinformatics</a>, <a href="https://groverj3.github.io/tag/data-visualization.html">data-visualization</a>
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<p><a href="/articles/2019-06-27_making-better-metaplots-with-ggplot-part-1.html">Last time</a> we
prepared our data using Deeptools.</p>
<p>Now we're going to do something kind of scandalous. R and python, living together
in peace. What is this madness? I like R's ecosystem for manipulating data and
plotting with the <a href="https://www.tidyverse.org/">tidyverse</a>. It still requires some
tweaking, but with a bit of …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2019-06-28_making-better-metaplots-with-ggplot-part-2.html#making-better-metaplots-with-ggplot-part-2"> Continue reading
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<h2><a href="https://groverj3.github.io/articles/2019-06-27_making-better-metaplots-with-ggplot-part-1.html#making-better-metaplots-with-ggplot-part-1">Making Better Metaplots With ggplot, Part 1</a></h2>
<p>
Posted on Thu 27 June 2019 in <a href="https://groverj3.github.io/category/how-to.html">how-to</a>
• Tagged with
<a href="https://groverj3.github.io/tag/bioinformatics.html">bioinformatics</a>, <a href="https://groverj3.github.io/tag/data-visualization.html">data-visualization</a>
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<p>Commonly, in bioinformatics we're in the business of determining whether
something, be it gene expression, or DNA methylation, or splicing, etc. is
different between multiple conditions. Typically this would be done by comparing
those data and using some kind of statistical test. However, with the continued
advances in sequencing technologies …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2019-06-27_making-better-metaplots-with-ggplot-part-1.html#making-better-metaplots-with-ggplot-part-1"> Continue reading
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<h2><a href="https://groverj3.github.io/articles/2019-06-25_managing-software-on-a-multiuser-linux-system.html#managing-software-on-a-multiuser-linux-system">Managing Software on a Multiuser Linux System</a></h2>
<p>
Posted on Tue 25 June 2019 in <a href="https://groverj3.github.io/category/how-to.html">how-to</a>
• Tagged with
<a href="https://groverj3.github.io/tag/sysadmin.html">sysadmin</a>
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<p>When I started my Ph.D. I had a good amount of experience working in a Linux
environment on my own computers. Mostly as a hobby. My advisor had bought a small
server several years previous for a post-doc's project and I was offered this
system to use for my …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2019-06-25_managing-software-on-a-multiuser-linux-system.html#managing-software-on-a-multiuser-linux-system"> Continue reading
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<h2><a href="https://groverj3.github.io/articles/2019-06-15_setting-up-a-static-site-with-pelican-and-github-pages.html#setting-up-a-static-site-with-pelican-and-github-pages">Setting up a Static Site With Pelican and GitHub Pages</a></h2>
<p>
Posted on Sat 15 June 2019 in <a href="https://groverj3.github.io/category/how-to.html">how-to</a>
• Tagged with
<a href="https://groverj3.github.io/tag/tutorial.html">tutorial</a>, <a href="https://groverj3.github.io/tag/pelican.html">pelican</a>
</p>
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<p>In an effort to aid in my future job searching I decided I needed a
personal/professional website. It needed to look good, contain links to my
relevant social and job-search profiles, host some examples of work from my Ph.D.
, showcase my skillset, and host my CV. GitHub pages …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2019-06-15_setting-up-a-static-site-with-pelican-and-github-pages.html#setting-up-a-static-site-with-pelican-and-github-pages"> Continue reading
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