Rinnformatics (John Rinn teaching)

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John Rinn has developed a course in Bioinformatics for ANYONE and EVERYONE ! Data sciences for biology Course -- what is typically called bioinformatics -- J...

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Choose your own adventure More RNAseq and ATACseq data from Human Stem Cells (John Rinn Teaching)

We are all done !! Now let's KNIT our ATACseq Analyses. Let's compile our results! (John Rinn CGL)

Can we use DESEQ to find which peaks change upon exposure to dox Yes we can ! John Rinn Teaching

Are ATACseq peaks different between samples Do our peaks change due to Dox (John Rinn Teaching)

Where do our ATACseq Peaks Live Let's learn to map Peaks to Genome Features (John Rinn Teaching)

Do peaks overlap across samples Let's find out, using find_overlaps function (John Rinn Teaching)

What do our ATACseq Peak Files look like Let's Load them (Granges) and see ! (John Rinn Teaching)

Exploring the Genome in GRanges What is the biggest gene And much more (John Rinn Teaching)

The Genome in Ranges! Let's get our genes and other features of the Genome (John Rinn Teaching)

GRanges Our genome in Ranges! Introduction to Genomic Ranges (John Rinn Computational Genomics lab)

Let's explore Iranges a concept of where our ATACseq peaks start and stop.

ATACseq OUTPUT Files !

Input files to Run ATAC Sequencing Analysis !

Getting Raw with our Data ! Let's analyze RNAseq in the IGV genome browser (John Rinn Teaching)

Heating up our Data Analysis with Heat Map Visualization of our RNAseq data! (John Rinn Teaching)

Custom Function Bonus - making plots with one line of code! (John Rinn Computational Genomics Lab)

Plotting TPM values - while learning how to melt data (John Rinn Computational Genomics Lab)

GGPLOT (III) Getting familiar with all layers of GGPLOT! (John Rinn Computational Genomics Lab)

GGPLOT II Going deeper into analysis and figure making (John Rinn Computational Genomics Lab)

Making RNAseq FIgures ! (John Rinn Computational Genomics)

One script to run all the RNAseq Analyses (John Rinn Computational Genomics Lab)

Let's analyze our RNAseq data in TPM (transcripts per million). John Rinn Computational Genomics Lab

Let's now explore and analyze all our results! John Rinn Computational Genomics Lab

Extract all DESEQ results using a for-loop. John Rinn Computational Genomics Lab (CGL)

Let's explore the DESEQ results files ! John Rinn Computational Genomics Lab.

Time for DESEQ RNAseq Analysis! (John Rinn Computational Genomics Lab)

Let's make our DESEQ Sample Sheet! John Rinn Computational Genomics Lab

Let's read in our RNAseq data into R ! John Rinn Computational Genomics Lab

Package Delivery !! Let's start installing R packages !! John Rinn computational genomics lab.

CU Students R Studio PRO on FIji. John Rinn Computational Genomics Lab