index.Rmd

---
title: "Aaron's single-cell thoughts"
---

# Overview

A collection of thoughts related to single-cell data analysis, mostly for RNA sequencing.

# General

Broad thoughts about practices in single-cell data analysis, not specific to my own software.

**Comments:**

- [Quality control](general/quality-control.html)
- [Linearity](general/linearity.html)
- [Transformation](general/transformation.html)
- [Standardization](general/standardization.html)
- [Clustering](general/clustering.html)
- [Cellular detection rate](general/cdr.html)
- [Bootstrapping](general/bootstrapping.html)
- [Visualization](general/visualization.html)

**Links:**

- Effects of log-transformation at https://github.com/LTLA/PseudoCount2018
- Other imputation pitfalls at https://github.com/LTLA/Counterspell2018

# Software 

Justifications for some of the programming choices used in my own scRNA-seq data analysis software.

**Comments:**

- [Correlations](software/correlations/corsim.html) (`r BiocStyle::Biocpkg("scran")`)
- [Marker detection](software/marker_detection/comments.html) (`r BiocStyle::Biocpkg("scran")`)
- Doublet detection [by cluster](software/doublet_detection/bycluster.html) or [per cell](software/doublet_detection/bycell.html) (`r BiocStyle::Biocpkg("scran")`)

**Links:**

- Scaling normalization in https://github.com/MarioniLab/FurtherNorm2018
- HVG selection in https://github.com/LTLA/HVGDetection2018
- PC selection in https://github.com/LTLA/PCSelection2018
- MNN correction in https://github.com/MarioniLab/FurtherMNN2018

# Workflow

Justifications for some of the parameter choices and strategies in my scRNA-seq analysis workflows.

**Comments:**

- [Quality control](software/correlations/qc.html) (`r BiocStyle::Biocpkg("simpleSingleCell")`)
- [Cell cycle detection](software/marker_detection/cycling.html) (`r BiocStyle::Biocpkg("simpleSingleCell")`)

# Other

Some collected miscellaneous thoughts:

- [Research integrity](general/integrity.html)