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<h1>LVG Bioinfo resources list</h1>
<p class="lead">A list of bioinformatic resources and tools to get started with bioinfo at the LVG</p>
</div>
<div class="row marketing">
<div class="col-lg-12">
<h2 class='page-header'>COVID-19 update</h2>
<p>As all of us are working remotely in this early 2020, we revamped this page and added
a bunch of things to learn about bioinformatics from home. Notably we added a <b>Courses</b>
section and update all of the sections with new sources, heavily inspired by this
<a
href="https://www.reddit.com/r/bioinformatics/comments/fiwtwx/working_from_home_i_made_a_guide_to_help_wet_lab/">
reddit post</a> I must say, so please check it out.
</p>
<h2 class='page-header'>Unix</h2>
<ul>
<li><a href=https://www.youtube.com/watch?v=oxuRxtrO2Ag>Video: Very basics of the terminal</a> | Start from 0, if you never opened a terminal</li>
<li><a href=https://www.datacamp.com/community/tutorials/shell-commands-data-scientist>8 useful command line for data science</a> | head,sort,uniq etc...</li>
<li><a href='unix_cheatsheet.pdf'>Unix cheatsheet</a> | The famous PDF with basics commands for bioinfo</li>
<li><a href='http://www.ee.surrey.ac.uk/Teaching/Unix/'>UNIX complete tutorial</a> | Tutorial One, Two and Three are the basics</li>
<li><a href=http://edu.isb-sib.ch/pluginfile.php/2878/mod_resource/content/3/couselab-html/content.html> SIB tutorial</a> | Interactive tutorial about UNIX basics</li>
</ul>
<h2 class='page-header'>Bedtools</h2>
<p>For installing BEDtools, please do ask us to help you. Installation can be a bit tricky and you can <b>mess up</b> your computer.</p>
<ul>
<li><a href='http://bedtools.readthedocs.org/en/latest/content/bedtools-suite.html'>BEDTools suite</a> | List of all the bedtools tools with explanation</li>
<li><a href='http://quinlanlab.org/tutorials/bedtools/bedtools.html'>BEDTools tutorial</a> | Examples of main usages</li>
</ul>
<h2 class='page-header'>NGS and Omics analysis</h2>
<ul>
<li><a href='https://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/RNA'>Wikibooks on NGS</a> | Very complete wikibook about NGS data - <b>start here</b></li>
<li><a
href='http://www.sumanasinc.com/webcontent/animations/content/highthroughput2.html'>Video: High-Throughput Sequencing</a> | Small introduction video about sequencing</li>
<li><a href='https://www.hadriengourle.com/tutorials/'>Bioinfo tutorials</a> | Learn the file formats, the techniques and the analysis <b>start here</b></li>
</ul>
<h4>RNA-seq</h4>
<ul>
<li><a href='https://www.bioconductor.org/packages/devel/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html'>RNAseq easy as 123</a> | Full guide to RNAseq analysis with R </li>
<li><a href='http://rnaseq.uoregon.edu'>RNA-seqlopedia</a> | All you need to know about RNA-seq</li>
</ul>
<h4>ChIP-seq</h4>
<ul>
<li><a href='https://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course/gene-regulation/chip-seq-analysis'>ChIP-seq talk</a> | Talk by Remco Loos from the EMBL-EBI (slides+vid); old but useful</li>
<li><a href='https://www.youtube.com/watch?v=Ob9xGBPvr_s'>Complete MIT OpenCourse </a> | Detailed course on ChIP-seq; full of math but start from the beginning</li>
</ul>
<h2 class='page-header'>Programming language</h2>
<p>At some point, you have to dive in... An advice I would give you is: try to have a
small project you would like to do which requires a bit of coding. The learning curve is
a <a style='font-size: 100%' href='learningcurve.png'>sigmoid function</a> which means
you will struggle a <b>LOT</b> at the beginning. Having a project keeps you motivated and
there is nothing more rewarding than to finally solve all the problems you had an
complete your project. One idea could be to get one of your RNAseq count table in R, and
do the things you'd do in excel using R only. Do some plots, do some stats etc... It's
important to realize that if you know 1 programming language, you learn the next one very
fast.</p>
<li><a href='https://www.codecademy.com/'>Codeacademy - Learn to code interactively</a> | Learn different languages interactively</li>
<h4>Python</h4>
<ul>
<li><a href='https://wiki.python.org/moin/BeginnersGuide'>Python Beginner Guide</a> | Official python's wiki</li>
<li><a href='http://www.learnpython.org/'>Python interactive tuto</a> | Try python and learn at the same time; easiest to start</li>
<li><a href='http://learnpythonthehardway.org/book/'>Learn python the hard way</a> | Probably one of the best method, but also the hardest... <u>start to finish</u></li>
<li><a href='https://www.datacamp.com'>Datacamp - lilke military camp but better</a> | Interactive course in the browser for data analysis</li>
</ul>
<h4>R</h4>
<ul>
<li><a href='http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual'>R Bioconductor manual</a> | Very good R manual from bioconductor; good but hard to read</li>
<li><a href='https://cran.r-project.org/doc/manuals/R-intro.pdf'>Official manual</a> | Standard R manual</li>
<li><a href='http://tryr.codeschool.com/levels/1/challenges/2'>Interactice tutorial</a> | Learn R basics easily and interactively</li>
<li><a href='http://swirlstats.com/'>Swirl - Learn R, in R</a> | Package to learn R basics directly in R</li>
<li><a href='https://www.datacamp.com'>Datacamp - lilke military camp but better</a> | Interactive course in the browser for data analysis</li>
<li><a href='http://adv-r.had.co.nz/'>Advanced R</a> | Become almost as good as Evarist with R</li>
<li><a href='https://serialmentor.com/dataviz/index.html'>Fundamentals of data Visualization </a> | Stop using the wrong plot for the data, no pie chart anymore</li>
<li><a href='https://r-graphics.org/'>R Graphic cookbook</a> | You want to do a plot, but don't know how?</li>
</ul>
<h2 class='page-header'>Books</h2>
<ul>
<li><a href='https://genomicsclass.github.io/book/'>Biomedical Data Science</a> | This book will cover several of the statistical concepts and data analytic skills needed to succeed in data-driven life science research</li>
</ul>
<h2 class='page-header'>Machine learning, AI and all other synonyms</h2>
<ul>
<li><a href='https://towardsdatascience.com/machine-learning-an-introduction-23b84d51e6d0'>Intro to ML</a> | Very soft intro to ML, learn the terms and concepts, no math, easy</li>
<li><a href='https://www.r-bloggers.com/in-depth-introduction-to-machine-learning-in-15-hours-of-expert-videos/'>15 hours intro to ML</a> | Video: All free on YT with expert explaining ML from easy to
wtf</li>
</ul>
<h2 class='page-header'>Courses</h2>
<p>If you are more of a course person, they are plenty of courses available online. I'd
suggest to first look into the R tutorials to have a basic idea about programming before
taking anything. Programming is a "do" thing, the more you do, the more you know.</p>
Find online courses on <a href="https://www.coursera.org">coursera</a>, <a
href="https://www.extensionschool.ch">EPFL Extension school</a>, <a href=https://www.freecodecamp.org/news/>freecodecamp</a> and <a
href="https://www.edx.org">Mooc/edx</a>. Please note I've not taken any of these courses, it's only suggestions related to what we do in the lab.
<h4>Basics</h4>
<ul>
<li><a href='https://www.coursera.org/learn/python'>Basic programming with python</a> | If you never ever programmed, it assumes 0 prior knowledge.</li>
<li><a href='https://www.edx.org/course/data-science-r-basics'>R basics</a> | Start to learn R, it assumes 0 prior knowledge.</li>
<li><a href='https://www.edx.org/course/statistical-analysis-in-bioinformatics-2'>Statistical analysis in biofino</a> | Learn the secrets of gene expression analysis with R</li>
<li><a
href='https://www.edx.org/course/i-heart-stats-learning-to-love-statistics'>Statistics
without math</a> | Do you love stats? You will soon</li>
</ul>
<h4>Intermediate</h4>
<ul>
<li><a href='https://www.extensionschool.ch/courses-and-programs'>EPFL extension school</a> | 7 courses at the moment that might be interesting. Check the program because it's not directly related to bioinfo</li>
<li><a href='https://www.classcentral.com/course/edx-statistics-and-r-2960?utm_source=fcc_medium&utm_medium=web&utm_campaign=ivy_league_courses_2020'>Statistics and R</a> | Apply statistics with R in the context of life Science. Better if you know a bit R before.</li>
<li><a href='https://www.edx.org/course/fundamentals-of-statistics'>Fundamentals of stats</a> | Learn some stats, but you should know some basic R first, and a bit of
math</li>
</ul>
<h2 class='page-header'>Other but very useful</h2>
<ul>
<li><a href='http://www.google.ch'>Google</a> | Everything has already been done; you'll discover stack overflow, biostar and so on...</li>
<li><a href='http://rosalind.info/problems/locations/'>Rosalind</a> | Platform to learn and train bioinfo; full of small exercises to learn</li>
</ul>
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