Bioinformatics Quick Look at Counts and Setting Up R Project

>> YOUR LINK HERE: ___ http://youtube.com/watch?v=hYI7bXwrXGI

Hey Everyone! Happy October! • Today we pick up where we left off after creating our counts file and moving over to R. • When we edit the counts file we can look at it using a tool called iDEP - http://bioinformatics.sdstate.edu/idep/ which is pretty easy to click through and visualize our data. I like the programming side of things so I will show how to do things in R Studio. • iDEP BMC Publication: • https://bmcbioinformatics.biomedcentr... • R can be downloaded from Cran (cran.r-project.org/). This is the base statistical programming language. R can be run alone but can also be run in a nicer looking manner with R Studio (rstudio.com). I will be using R Studio here and recommend it due to it's great interface. • R Packages: • BiocManager • dplyr • gplots • ggplot2 • ggrepel • BiocManager Packages: • limma • DESeq2 • AnnotationDbi • org.Mm.eg.db • ReportingTools • GO.db • GOstats • pathview • gage • gageData • select • Project Github: • https://github.com/ACSoupir/Bioinform... • GitHub Link to zipped R Project: • https://github.com/ACSoupir/Bioinform... • • I'm not an expert in bioinformatics, this is just the way that I do things although there may be slightly better ways to do things. I use these videos as teaching experience and to hear from others in the community in an open discussion because we all can learn from each other which is what makes it fun!Image at the beginning on the bottom left is modified from AllGenetics.EU • Please consider contributing to my Patreon where I may do merch and gather ideas for future content: • / alexsoupir

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