nilseling / thesis

Latex scripts to compile my PhD thesis

My work focuses on single-cell, bioimage and spatial data analysis to understand immune-tumor interactions in various cancer types. I also build R/Bioconductor packages and workflows to standardize bioimage and spatial data analysis. You can see my main contributions on the BodenmillerGroup organisation.

GitHub statistics

Ex-Package maintainer

Package	Rank	Build
cytomapper
imcRtools

Package contributor

Package	Rank	Build
cytoviewer
BASiCS
imcdatasets

Ex-Workflow maintainer

Workflow	Build	Website
IMCWorkflow		https://bodenmillergroup.github.io/IMCWorkflow/
IMCDataAnalysis		https://github.com/BodenmillerGroup/IMCDataAnalysis

Analysis repositories

Repository	Year
cytomapper_publication	2020
GammaDeltaTcells2018	2018
Spermatogenesis2018	2018
RegressionBASiCS2017	2017
ImmuneAging2017	2017
Platynereis2017	2017

thesis's Issues

Check for broken references

Sort out formatting

• Figures in right place
• reduce whitespace
• Headings for Abstract, Declaration, TOF, ...

Generate figures for introduction

Write declaration

Using we and I to indicate what has been done only by me

Check appendix

Check for American and British English

Write CyTOF intro

Things to correct

"Cell-type" to "cell type"

Fix nomenclature

Go through refernces

Correct tense

Write Acknowledgements