https://github.com/christianholland/thesis

My PhD thesis
https://github.com/christianholland/thesis

bookdown phd r thesis

Last synced: over 1 year ago
JSON representation

My PhD thesis

• Host: GitHub
• URL: https://github.com/christianholland/thesis
• Owner: christianholland
• License: gpl-3.0
• Created: 2020-05-10T18:20:10.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2022-07-11T15:36:02.000Z (almost 4 years ago)
• Last Synced: 2025-01-22T07:52:57.311Z (over 1 year ago)
• Topics: bookdown, phd, r, thesis
• Language: TeX
• Homepage: https://christianholland-thesis.netlify.app
• Size: 40.5 MB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE
  • Citation: CITATION.cff

Awesome Lists containing this project

README

          
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>"

)

```

# My PhD thesis

[![Netlify Status](https://api.netlify.com/api/v1/badges/a71856c3-c83a-4be6-aa3b-642e0e3ec82e/deploy-status)](https://app.netlify.com/sites/christianholland-thesis/deploys)

## From gene expression to pathway and transcription factor activities to study chronic liver diseases

This thesis is based on three manuscripts each forming a separate chapter. An online version of this thesis can be accessed at [Netlify](https://christianholland-thesis.netlify.app).

### Chapter 1

Transfer of regulatory knowledge from human to mouse for functional genomics analysis ([Publication](https://doi.org/10.1016/j.bbagrm.2019.194431), [GitHub repository](https://github.com/saezlab/ConservedFootprints)).

### Chapter 2

Robustness and applicability of transcription factor and pathway analysis tools 

on single-cell RNA-seq data ([Publication](https://doi.org/10.1186/s13059-020-1949-z), [GitHub repository](https://github.com/saezlab/FootprintMethods_on_scRNAseq)).

### Chapter 3

Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice ([Publication](https://doi.org/10.1002/hep4.1797), [GitHub repository](https://github.com/saezlab/liver-disease-atlas)).