2021_BRE
Repository for Coriell Institute's 2021 Bioinformatics Research Experience
Coriell Bioinformatics Research Experience 2021
The Bioinformatics Research Experience is a four-week research training program for undergraduate students interested in learning scientific biological data analysis. The previous year’s material can be seen here: 2020
Schedule
Talks and Lecture Topics
Getting Started
Programs to Install
- Zoom https://zoom.us/download
- Slack https://slack.com/. If you’re familiar with Slack, our slack name is coriellbioinf-se37156. Otherwise you can follow the attached directions in slack_intructions.pdf.
- Download and install TeamViewer https://www.teamviewer.com/en-us/. This will allow the research experience team to screen share with your computer to assist with technical problems.
- R. If you don’t already have it installed, go to R Cloud https://cloud.r-project.org/ to download and install R.
- RStudio. Go to RStudio’s website https://rstudio.com/products/rstudio/download/ and download the FREE version.
BRE Material
Journal Club
During the Bioinformatics Research Experience you will give two Journal Clubs, one on one of the papers listed below and the other on a paper of your choosing. Your choice of second paper is due by Friday, 7/16.
- Journal Club Sign Up GoogleSheet https://docs.google.com/spreadsheets/d/1jFC24C2OL5drmgdDU9ApuyTB8uDavt9VfCs84Gnn6mg/edit?usp=sharing
- Examples
- Old Coriell journal club slides
- YouTube Video https://www.youtube.com/watch?v=xXKL9uLFHy4
- Papers
- Cani 2018 Microbiome
- Greenberg 2019 Methylation
- Kazazian 2017 Repetitive/Transposable Elements
- Klemm 2019 Chromation Accessibility
- Stark 2019 RNA-seq
- Tang 2019 Single Cell Sequencing
Daily Lecture Material
July 06: Welcome and Introduction to Rmarkdown and RStudio
- Introduction to Coriell and Coriell’s Bioinformatics Research Experience
- Introduction to Rmarkdown and RStudio
- slides
- demo Rmd and its knitted html
Today’s Assignment: Rmarkdown Practice Rmarkdown and the ANSWER KEY in Rmarkdown and html
July 07: Introduction to Data Wrangling with dplyr
- Examing and subsetting data with base
R - Data wrangling with
dplyr - slides
- demo Rmd and updated demo Rmd with in class additions
Today’s Assignment: Data Wrangling Rmarkdown, ANSWER KEY in Rmarkdown
July 08: Introduction to Data Visualization with ggplot2
- Data visualization with
ggplot2 - slides
- demo Rmd and demo Rmd with in class additions
- Resources
- R Graph Gallery https://www.r-graph-gallery.com/
- R Color Chart
Today’s Assignment: Data Visualization Rmarkdown, ANSWER KEY in Rmarkdown
July 09: Reading Data with readr and Tidying Data with tidyr
- How to read data into
Rusingreadr - More data wrangling, tidying data with
tidyr - slides
- demo Rmd and demo Rmd with in class additions
- demo data
Today’s Assignment: Reading in and Tidying Data Rmarkdown and the data, ANSWER KEY in Rmarkdown
July 13: Statistics Review and Tidying R Statistical Tests with broom
- Basic Statistical Tests
- t-test
- chi-square
- ANOVA
- Transforming R test results into tidy tables with
broom - slides
- demo Rmd and demo Rmd with in class additions
Today’s Assignment: Statistics and broom Rmarkdown and the data, ANSWER KEY in Rmarkdown
July 14: Clustering Data
- Clustering
- kmeans clustering
- hierarchical clustering with heatmaps
- Principal Component Analysis (PCA)
- slides
- demo Rmd
Today’s Assignment: Clustering Rmarkdown and the data, ANSWER KEY in Rmarkdown
July 15: Statistics 2: Linear Models
- linear models
- calculation and interpretation
- multiple variables, both additive and interactive
- selecting the best model
- slides
- demo Rmd
- and demo Rmd with in class additions
- demo data
Today’s Assignment: Linear Models Rmarkdown and the data, ANSWER KEY in Rmarkdown
July 16: Exploratory Data Analysis
Today’s Assignment: Exploratory Data Analysis assignment and the template
- example Rmd and example data
- Tidy Tuesday https://github.com/rfordatascience/tidytuesday
July 20: Introduction to RNA-seq
- Introduction to RNA-seq
- Lab process and considerations for RNA-seq
- Overview of processing RNA-seq data
- General analysis description
- single cell RNA-seq
- Reading and wrangling RNA-seq data in R
- slides
- demo Rmd and with in class changes
- demo data
Today’s Assignment: Read in RNA-seq Data Rmd and the data, , ANSWER KEY in Rmarkdown
July 21: Clustering RNA-seq and Differential Expression Testing
- normalizing RNA-seq counts
- Nice overview of RNA-seq normalization and the different normalized counts https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html
- clustering
- differential expression testing
- slides
- demo Rmd and with in class addtions Rmd
- Same demo data
Today’s Assignment: Read in RNA-seq Data Rmd and the same data and the ANSWER KEY in Rmarkdown
July 22: Wrangling and Visualizing RNA-seq Results
- wrangling differential expression results
- MA plots
- volcano plots
- UpSet plots
- slides
- demo Rmd and with in class addtions Rmd
- This uses the differential expression table created in yesterday’s demo, but it’s here as well
Today’s Assignment: Read in RNA-seq Data Rmd and you’ll use for data the differential expression table you created with yesterday’s assignment and here’s the ANSWER KEY in Rmarkdown
July 23: Review Day
July 27: Gene Set Enrichment Analysis
Differential Expression Assignment
- assignment
- Go to https://docs.google.com/spreadsheets/d/1dal19nICrX4PoVzh_rjLUfnR1PmBom_JwmGS8A3uPQc/edit?usp=sharing to sign up for a dataset and for a time to practice your RNA-seq presentation
- example presentation slides
July 28 Regular Expressions (RegEx)
- demo Rmd and with in class additions Rmd
- R Cheat Sheets https://www.rstudio.com/resources/cheatsheets/
July 29 Example RNA-seq Results Presentation
- exmample presentation pdf