Example homework assignment

Warning

This is not a real assignment for CSCB! It's just a realistic example to demonstrate the style guide.

Goal

The goal of this assignment is to give you some experience in data wrangling and quality control of scRNA-seq data.

Due date: Jan 1st, 2001.

Data

In this assignment, you will perform a few initial steps in the analysis of a dataset from a tech-dev paper showing off an unusual combination of cababilities. The paper includes several large experiments with genetic perturbations followed by a scRNA-seq readout (Replogle et al 2020). These assays are applied to mostly the K562 leukemia cell line. We'll focus on just the CRISPRa multiplexing experiment, which does gene overexpression followed by scRNA.

Your mission

Task 1

• Tidy the dataset so that it fits in an AnnData object.
• For each overexpressed gene, how many cells are measured?

Task 2

• Compute typical scRNA quality metrics and filter out genes and cells as discussed in class.
• As you apply each filter, print the number of cells remaining so that anyone following your code can see which filtering steps are most impactful.

Task 3

• Write code to visualize the data using scanpy.
• Run the code and describe the results.

Resources

You may use the provided code (ingestion.py) to convert gene names from Ensembl gene id's (example: ENSG00000109101) to more readable Entrez gene symbols (example: Foxn1).

Deliverables

A Jupyter notebook that contains documented code achieving Tasks 1, 2, and 3. For an example submission, [['HWEX Done']].