-
Notifications
You must be signed in to change notification settings - Fork 0
/
blog.html
377 lines (311 loc) · 17.8 KB
/
blog.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="HandheldFriendly" content="True" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<meta name="robots" content="" />
<link href="https://fonts.googleapis.com/css?family=Source+Code+Pro|Source+Sans+Pro:300,400,400i,700" rel="stylesheet">
<link rel="stylesheet" type="text/css" href="https://groverj3.github.io/theme/stylesheet/style.min.css">
<link rel="stylesheet" type="text/css" href="https://groverj3.github.io/theme/pygments/paraiso-dark.min.css">
<link rel="stylesheet" type="text/css" href="https://groverj3.github.io/theme/font-awesome/css/fontawesome.css">
<link rel="stylesheet" type="text/css" href="https://groverj3.github.io/theme/font-awesome/css/brands.css">
<link rel="stylesheet" type="text/css" href="https://groverj3.github.io/theme/font-awesome/css/solid.css">
<link href="https://groverj3.github.io/feeds/all.atom.xml" type="application/atom+xml" rel="alternate" title="Jeff Grover. Bioinformatics Scientist. Atom">
<meta name="author" content="Jeffrey Grover" />
<meta name="description" content="" />
<meta property="og:site_name" content="Jeff Grover. Bioinformatics Scientist."/>
<meta property="og:type" content="blog"/>
<meta property="og:title" content="Jeff Grover. Bioinformatics Scientist."/>
<meta property="og:description" content=""/>
<meta property="og:locale" content="en_US"/>
<meta property="og:url" content="https://groverj3.github.io"/>
<meta property="og:image" content="/images/jeff.jpg">
<title>Jeff Grover. Bioinformatics Scientist.</title>
</head>
<body>
<aside>
<div>
<a href="https://groverj3.github.io">
<img src="/images/jeff.jpg" alt="Jeffrey Grover" title="Jeffrey Grover">
</a>
<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>
<nav>
<ul class="list">
<li><a href="/pages/about.html">About</a></li>
<li><a href="/blog.html">Blog</a></li>
<li><a href="/pages/cv.html">CV</a></li>
<li><a href="/pages/projects.html">Projects</a></li>
</ul>
</nav>
<ul class="social">
<li>
<a class="sc-envelope" href="mailto:jeffrey.w.grover@protonmail.com" target="_blank">
<i class="fas fa-envelope">
</i>
</a></li>
<li>
<a class="sc-linkedin" href="https://www.linkedin.com/in/jeffreygrover/" target="_blank">
<i class="fab fa-linkedin">
</i>
</a></li>
<li>
<a class="sc-github" href="https://github.com/groverj3" target="_blank">
<i class="fab fa-github">
</i>
</a></li>
</ul>
</div>
</aside>
<main>
<nav>
<a href="https://groverj3.github.io"> Home
</a>
<a href="/pages/about.html">About</a>
<a href="/blog.html">Blog</a>
<a href="/categories.html">Categories</a>
<a href="/tags.html">Tags</a>
<a href="https://groverj3.github.io/feeds/all.atom.xml"> Atom
</a>
</nav>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2024-06-02_polyglot-r-and-python-bioinformatics-and-data-science-projects-using-jupyter-notebooks.html#polyglot-r-and-python-bioinformatics-and-data-science-projects-using-jupyter-notebooks">Polyglot R and Python Bioinformatics and Data Science Projects Using Jupyter Notebooks</a></h2>
<p>
Posted on Sun 02 June 2024 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/jupyter.html">jupyter</a>, <a href="https://groverj3.github.io/tag/notebooks.html">notebooks</a>, <a href="https://groverj3.github.io/tag/tutorial.html">tutorial</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/sysadmin.html">sysadmin</a>
</p>
</header>
<div>
<p>TLDR - Check out this github repo for a (still really wordy) example:
<a href="https://github.com/groverj3/polyglot_jupyter_example">polyglot_jupyter_example</a></p>
<p>If you're anything like me, and there are probably tens of you out there, you
enjoy working in multiple programming languages for your bioinformatics/data
science work. Perhaps you love the <a href="https://www.tidyverse.org/">tidyverse</a> R
ecosystem for data manipulation …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2024-06-02_polyglot-r-and-python-bioinformatics-and-data-science-projects-using-jupyter-notebooks.html#polyglot-r-and-python-bioinformatics-and-data-science-projects-using-jupyter-notebooks"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2024-05-24_nextflow-with-first-class-metadata-a-minimal-example.html#nextflow-with-first-class-metadata-a-minimal-example">Nextflow With First Class Metadata: A Minimal Example</a></h2>
<p>
Posted on Fri 24 May 2024 in <a href="https://groverj3.github.io/category/how-to.html">how-to</a>
• Tagged with
<a href="https://groverj3.github.io/tag/workflows.html">workflows</a>, <a href="https://groverj3.github.io/tag/bioinformatics.html">bioinformatics</a>, <a href="https://groverj3.github.io/tag/rnaseq.html">RNAseq</a>
</p>
</header>
<div>
<p>TLDR - Check out this github repo for the full example:
<a href="https://github.com/groverj3/minimal_nextflow_samplesheet_example">https://github.com/groverj3/minimal_nextflow_samplesheet_example</a></p>
<p>I recently wrote <a href="2024-04-26_on-bioinformatics-workflow-design.html">an article</a>
regarding some of my opinions on bioinformatics workflow design. I've written
workflows in several languages over the years, but at this point it seems that
<a href="https://www.nextflow.io/">Nextflow</a> has become something of …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2024-05-24_nextflow-with-first-class-metadata-a-minimal-example.html#nextflow-with-first-class-metadata-a-minimal-example"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2024-05-04_bridging-the-gap-with-wet-lab-using-r-shiny.html#bridging-the-gap-with-wet-lab-using-r-shiny">Bridging the Gap With Wet Lab Using R Shiny</a></h2>
<p>
Posted on Sat 04 May 2024 in <a href="https://groverj3.github.io/category/how-to.html">how-to</a>
• Tagged with
<a href="https://groverj3.github.io/tag/r.html">R</a>, <a href="https://groverj3.github.io/tag/shiny.html">shiny</a>, <a href="https://groverj3.github.io/tag/app.html">app</a>, <a href="https://groverj3.github.io/tag/rnaseq.html">RNAseq</a>, <a href="https://groverj3.github.io/tag/bioinformatics.html">bioinformatics</a>, <a href="https://groverj3.github.io/tag/data-visualization.html">data-visualization</a>
</p>
</header>
<div>
<p>How do you communicate results of an analysis? What tools do you use?
Scientists that work in the wet lab are accustomed to firing up excel or some
instrument-specific software and working with their own data. For genomics
or other types of experiments in biology that result in large datasets …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2024-05-04_bridging-the-gap-with-wet-lab-using-r-shiny.html#bridging-the-gap-with-wet-lab-using-r-shiny"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2024-04-26_on-bioinformatics-workflow-design.html#on-bioinformatics-workflow-design">On Bioinformatics Workflow Design</a></h2>
<p>
Posted on Fri 26 April 2024 in <a href="https://groverj3.github.io/category/commentary.html">commentary</a>
• Tagged with
<a href="https://groverj3.github.io/tag/workflows.html">workflows</a>, <a href="https://groverj3.github.io/tag/bioinformatics.html">bioinformatics</a>
</p>
</header>
<div>
<p>Since I was in grad school I've been writing bioinformatics <a href="2019-08-19_the-snakemake-tutorial-i-wish-i-had.html">workflows</a>.
Usually to process NGS data. The concept of a workflow is simple, <a href="https://github.com/spotify/luigi">and not limited to the domain of bioinformatics</a>.
However, a workflow (aka "pipeline") used to analyze data from next generation sequencing (again, will it ever be
"current …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2024-04-26_on-bioinformatics-workflow-design.html#on-bioinformatics-workflow-design"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2024-04-21_making-volcano-plots-with-ggplot2.html#making-volcano-plots-with-ggplot2">Making Volcano Plots With ggplot2</a></h2>
<p>
Posted on Sun 21 April 2024 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>, <a href="https://groverj3.github.io/tag/rnaseq.html">rnaseq</a>
</p>
</header>
<div>
<p>One of the, if not <em>the</em>, most common downstream analysis task I'm asked to perform on RNAseq data is to generate the
venerable "Volcano Plot." These are kind of the bioinformatics equivalent of saying "Hey! Look how much data I have!"
Regardless, they are a pretty good way to quickly …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2024-04-21_making-volcano-plots-with-ggplot2.html#making-volcano-plots-with-ggplot2"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2024-04-20_managing-software-on-a-multiuser-linux-system-an-update.html#managing-software-on-a-multiuser-linux-system-an-update">Managing Software on a Multiuser Linux System - An Update</a></h2>
<p>
Posted on Sat 20 April 2024 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>
</p>
</header>
<div>
<p>Back in 2019, the halcyon days of yore, near the end of my time in graduate school I wrote a well-intentioned article
about software management for multi-user linux systems (<a href="/articles/2019-06-25_managing-software-on-a-multiuser-linux-system.html">here</a>).
This original article was written based on my experiences as the de-facto sysadmin of our lab's bioinformatics server.
I am …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2024-04-20_managing-software-on-a-multiuser-linux-system-an-update.html#managing-software-on-a-multiuser-linux-system-an-update"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2020-05-30_publications-dissertations-job-hunts-and-a-pandemic.html#publications-dissertations-job-hunts-and-a-pandemic">Publications, Dissertations, Job Hunts, and a Pandemic</a></h2>
<p>
Posted on Sat 30 May 2020 in <a href="https://groverj3.github.io/category/commentary.html">commentary</a>
• Tagged with
<a href="https://groverj3.github.io/tag/grad-school.html">grad school</a>, <a href="https://groverj3.github.io/tag/jobs.html">jobs</a>
</p>
</header>
<div>
<p>I started this github site as a place to expand my professional reach by posting
my random musings on bioinformatics, Linux, data science, and etc. I made a few
reasonably cogent posts, but then life got in the way! It's been a really busy
time, a very eventful year. I'm …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2020-05-30_publications-dissertations-job-hunts-and-a-pandemic.html#publications-dissertations-job-hunts-and-a-pandemic"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2019-08-22_just-write-your-own-python-parsers-for-fastq-files.html#just-write-your-own-python-parsers-for-fastq-files">Just Write Your Own Python Parsers for .fastq Files</a></h2>
<p>
Posted on Thu 22 August 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/python.html">python</a>, <a href="https://groverj3.github.io/tag/workflows.html">workflows</a>
</p>
</header>
<div>
<p>In contrast to the <a href="https://en.wikipedia.org/wiki/Zen_of_Python">zen of python</a>
there are actually many ways to handle sequence data in Python. There are several
packages on <a href="https://pypi.org">PyPI</a> that provide parsers for sequence formats
like .fastq and .fasta. I've never bothered with these, including the oft-used
<a href="https://biopython.org">Biopython</a>. I vaguely remembered Biopython being slower
than …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2019-08-22_just-write-your-own-python-parsers-for-fastq-files.html#just-write-your-own-python-parsers-for-fastq-files"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2019-08-19_the-snakemake-tutorial-i-wish-i-had.html#the-snakemake-tutorial-i-wish-i-had">The Snakemake Tutorial I Wish I Had</a></h2>
<p>
Posted on Mon 19 August 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/python.html">python</a>, <a href="https://groverj3.github.io/tag/workflows.html">workflows</a>, <a href="https://groverj3.github.io/tag/snakemake.html">snakemake</a>
</p>
</header>
<div>
<p>Over the past few years the use of workflow managers in genomics and
bioinformatics has grown greatly. This is a great thing for the field and adds to
our ability to perform reproducible analyses, especially for pipelines with many
steps. These are common in bioinformatics, but prior to the use …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2019-08-19_the-snakemake-tutorial-i-wish-i-had.html#the-snakemake-tutorial-i-wish-i-had"> Continue reading
</a>
</div>
<hr />
</article>
<article>
<header>
<h2><a href="https://groverj3.github.io/articles/2019-08-09_suggestions-for-reproducible-bioinformatic-analyses.html#suggestions-for-reproducible-bioinformatic-analyses">Suggestions for Reproducible Bioinformatic Analyses</a></h2>
<p>
Posted on Fri 09 August 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/workflows.html">workflows</a>
</p>
</header>
<div>
<p>Bioinformatic analyses often require lengthy workflows or pipleines, where the
output of program A feeds into program B, and so on. These programs may also not
output their results in a format which is convenient to use in the subsequent
steps, requiring writing a conversion script, or piping its output …</p>
<br>
<a class="btn" href="https://groverj3.github.io/articles/2019-08-09_suggestions-for-reproducible-bioinformatic-analyses.html#suggestions-for-reproducible-bioinformatic-analyses"> Continue reading
</a>
</div>
</article>
<div class="pagination">
<a class="btn float-left" href="https://groverj3.github.io/blog2.html">
<i class="fa fa-angle-left"></i> Older Posts
</a>
</div>
<footer>
<p>
© 2019 - This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International License</a>
</p>
<p> Powered by <a href="http://getpelican.com" target="_blank">Pelican</a> - <a href="https://github.com/alexandrevicenzi/flex" target="_blank">Flex</a> theme by <a href="http://alexandrevicenzi.com" target="_blank">Alexandre Vicenzi</a>
</p><p>
<a rel="license"
href="http://creativecommons.org/licenses/by-sa/4.0/"
target="_blank">
<img alt="Creative Commons License"
title="Creative Commons License"
style="border-width:0"
src="https://i.creativecommons.org/l/by-sa/4.0/80x15.png"
width="80"
height="15"/>
</a>
</p> </footer>
</main>
<script type="application/ld+json">
{
"@context" : "http://schema.org",
"@type" : "Blog",
"name": " Jeff Grover. Bioinformatics Scientist. ",
"url" : "https://groverj3.github.io",
"image": "/images/jeff.jpg",
"description": ""
}
</script>
</body>
</html>