Muhammad's office hours are: MTW 10am to 1pm, Thursday 1pm to 2pm in Root Hall A-015.
Click on the links on the left for information about the course.
Here I'll keep notes on announcements for the course.
Skip to the latest
- May 22
- For the R programming workshops (see BD4ISU calendar), we are giving everyone a cs299xy account on the CS systems so that you can use R installed on the CS systems. The username and password are given in the BD4ISU blackboard site. If you haven't been added to the blackboard site, ask Jeff or Muhammad to add you.
First task - get your username and password from blackboard and login to the system
you are sitting at.
Second task - open up the terminal, and use the passwd command to change the password to something you will remember.
Third task - make sure you know how to open a web browser and how to logout of the system.
Fourth task - get started in the Linux and CS Systems Bootcamp (link also is on the links page).
- Next once you do all that - be reading through the information on the linux bootcamp, and check the assignments. For the assignments we will be checking those to make sure you get them correct. Please do those in your cs299xy account so we can check your answers.
- Last, make sure you have installed the software you need to in order to login to the CS server remotely (see here).
- Last, last, start reading the information listed at R Programming Bootcamp (note that this is being currently created, check back on May 22) and R programming links off of the links page. Start looking at the Gene Expression in Developing Heart Cells example and see how much you can understand. What questions do you have about the data? About the R code? Questions that you think we can answer based on what we can do so far in R?
- Questions from yesterday?
- Setting up putty, winscp/filezilla on your laptop, and transferring files from CS server. Setting up R, Rstudio on your laptop.
- R programming bootcamp - slides, basics quizzes, case study.
- Assignment 4 - new quizzes, created by Muhammad.
- Assignment 5 - something with gene expression data.
- Note - no meeting on Monday, we're off for memorial day.
- Gene expression case study - differential expression package and use
- Jeff's solution to assignment 5. Going further with that.
- Maybe - Rmd
- Look back at the R Programming Bootcamp. Review the R Getting Started Slides.
- From the R Programming Bootcamp, look at the quiz R files, and think about what you think each line will output. And we run them together.
- Gene expression dataset - let's look at GSE69618 - get it from the "In Class Code" link, load it, let's take a look.
- Rmd file to look at and play with - randomSamples.Rmd in the "In Class Code" link.
- The CarDGEA app - https://gitlab.com/jkinne/isu-gene-analysis - anything that happens in that app we know how to do...
- Jeff make up some slides about "visualization" and different types of plots and such - plot, hist, boxplot, points, lines.
- For fun - histogram of occurrence of numbers in wikipedia (or other sources).
- Exercise of conditional probability - diagnostic tests, how that raises/lowers probability of disease, also examples of culpability of crimes, etc.
- Gene differential expression analysis with limma, etc.
- Maybe - Shiny