```{r}
#| label: plotting-code-by-jay-h
#| eval: false
ggplot(mtcars, aes(hp, mpg)) + geom_point()
```MOLB 7950 – Final Projects
Short proposal
Please submit a short proposal for your final projects with the following information.
the names of people you are working with
a description of the data set you will be working worth. This can refer to a publication and/or contain a link to public data available at NCBI GEO.
a hypothesis (tentative) you will be testing
a few bullets on your planned analysis approach.
Please include this information in a quarto document in a new Posit cloud project.
Overview
Final projects can involve groups of 1-3 people.
Projects are choose your own adventure:
The resource documents contain data sets in from human S. cerevisiae. For example, sub-nucleosomal fragments provide a DNA-based signal to understand chromatin transactions that lead to transcription.
You could find a data set on NCBI GEO of interest (e.g., relevant to your thesis work), and work it up with salmon, DEseq, and exploratory analysis. We are happy to help you work through the pseudo-alignment steps.
You can start with your own sequencing data (bulk/single-cell RNA seq, DNA sequencing).
Deliverables
A Quarto document with code, plots, interpretations, and next steps.
If you work in a group, list the members of the group at the top of the document, and make it clear which parts are your work by adding your initials to code chunks.
Short presentations (5-8 minutes) by the groups the week of Nov 1. Presentations should include 1-2 slides of background, a hypothesis for the approach, code output (table or graph) that addresses the hypothesis, and one or more tests of the statistical significance of the observation.
Grading and rubric
The final project will be worth 20% of your grade and we will use the grading scheme outlined in the grading rubric.
Each individual in a group will be evaluated separately, so contributions must be clearly marked in the document, using e.g. using chunk labels: