---
title: "Hang's rotation-2 log"
site: workflowr::wflow_site
output:
  workflowr::wflow_html:
    toc: false
editor_options:
  chunk_output_type: console
---

![](https://raw.githubusercontent.com/chenh19/rotation2/main/analysis/images/header.jpg)

## GTD

[**Project-1: STING-seq**](https://chenh19.github.io/rotation2/project_1.html)

- [x] read Morris *et al.* 2021
- [x] read Morris *et al.* 2021 **again**
- [x] read Yalamanchili *et al.* 2017
- [x] perform fastqc on demuxed fastq files
- [x] know what else QC should be done (roughly)
- [x] overview before QC
- [x] read Luecken *et al.* 2019
- [x] perform QC (learn Seurat functions, such as filtering out mito genes)
- [x] check QC'ed scRNA-seq data (expression distribution)
- [x] re-do QC (UMI>=1400)

[**Project-2: SCEPTRE**](https://chenh19.github.io/rotation2/project_2.html)

- [x] read Barry *et al.* 2021
- [x] perform association analysis (*cis*-regulation; negative control; naive negative binomial; with total_UMI cov)
- [x] QQ-plot
- [ ] p-value distribution
- [ ] debug SCEPTRE

[**Miscellaneous:**](https://chenh19.github.io/rotation2/misc.html)

- [x] organize all logistics
- [x] organize all code into separate scripts
